Toll-like receptor 5 ligands and methods of use

ABSTRACT

The invention provides an immunomodulatory flagellin peptide having substantially the same amino acid sequence GALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQ (SEQ ID NO:44), or a modification thereof, and having toll like receptor 5 (TLR5) binding. The immunomodulatory flagellin peptide also can have substantially the same amino acid sequence TQFSGVKVLAQDNTLTIQVGANDGETIDIDLKQINS QTLGLDTL (SEQ ID NO:45); EGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVNG (SEQ ID NO:46) or MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANF TANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQS (SEQ ID NO:47), or a modification thereof. Also provided is an immunomodulatory flagellin peptide having substantially the same amino acid sequence LQKIDAALAQVDTLRSDLGAVQNRFNSAITNL (SEQ ID NO:48), or a modification thereof, and having toll like receptor 5 (TLR5) binding. The immunomodulatory flagellin peptide also can have substantially the same amino acid sequence TLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:49) or EQAAKTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:50), or a modification thereof. Further provided is an immunomodulatory flagellin peptide having substantially the same amino acid sequence GALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAE ITQ (SEQ ID NO:44) and substantially the same amino acid sequence LQKIDAALAQVDTLRSDLGAVQNRFNSAITNL (SEQ ID NO:48), or a modification thereof, and having toll like receptor 5 (TLR5) binding. Methods of using immunomodulatory flagellin peptides additionally are provided.

This application is a continuation-in-part of Ser. No. 10/125,692, filed Apr. 17, 2002, and is based on, and claims the benefit of, U.S. Provisional Application No. 60/285,477, filed Apr. 20, 2001, both of which are incorporated herein by reference.

This invention was made with government support under grant numbers 5R37AI025032 and 5R01AI032972, awarded by the National Institutes of Health. The United States Government has certain rights in this invention.

BACKGROUND OF THE INVENTION Reference to Sequence Listing Submitted Via EFS-WEB

The entire content of the following electronic submission of the sequence listing via the USPTO EFS-WEB server, as authorized and set forth in MPEP §1730 II.B.2(a)(C), is incorporated herein by reference in its entirety for all purposes. The sequence listing is identified on the electronically filed text file as follows:

File Name Date of Creation Size (bytes) 655652000220Seqlist.txt Nov. 20, 2009 153,610 bytes

Cancer is the second leading cause of death in the United States, accounting for one in every four deaths. This year, it is expected that over 1500 Americans will die of cancer each day and that a million new cases of cancer will be diagnosed. The most common treatments for cancer are surgery, radiation and chemotherapy. According to the American Cancer Society, immunotherapy can be considered as the “fourth modality” in the treatment of cancer. Immunotherapy is treatment that stimulates one's own immune system to fight cancer.

Cancer is a group of diseases characterized by uncontrolled growth of abnormal cells of the body. All types of cancer involve the malfunction of genes that control cell growth and division. Some of these genes become incorrectly regulated, resulting in over- or under-production of a particular protein, while others become mutated, resulting in unusual or abnormal proteins that alter normal cellular functions. These abnormal proteins, referred to as “tumor cell antigens,” should be recognized and destroyed by an individual's immune system as “foreign” antigens.

However, the immune system of a cancer patient may ignore these tumor antigens and be unresponsive to the growing tumor. Using immunotherapy approaches, such as cancer vaccines and immune system modulators, an individual's immune system can be induced to mount a potent immune response against tumor cell antigens, resulting in elimination of cancer cells. A cancer vaccine can contain a tumor cell antigen that stimulates the immune system to recognize and destroy cells which display that antigen. Treating an individual with such a cancer vaccine can result in a humoral response, which involves producing antibodies that recognize and target tumor cells for destruction and a cellular response, which involves producing cytotoxic T cells that recognize and destroy tumor cells directly, or both responses. It can be desirable to obtain both a humoral and cellular immunity response during immunotherapy because both arms of immune response have been positively correlated with beneficial clinical responses. To help stimulate either or both humoral and cellular immune responses, a cancer vaccine can be combined with an adjuvant, which is a substance that stimulates a general immune response.

The potency of cancer vaccines is greatly enhanced by the use of adjuvants. The selection of an adjuvant for use with a particular vaccine can have a beneficial effect on the clinical outcome of vaccination. Some vaccines are ineffective in the absence of an adjuvant. Effectiveness of a vaccine may be particularly troublesome when the vaccine is produced from self antigens such as those required for cancer vaccines or other non-infectious disease vaccines. In view of the beneficial effects of adjuvants in vaccine formulations, it is surprising that only one type of adjuvant, aluminum-salt based adjuvants, are currently in wide use in United States-licensed vaccines.

Thus, there exists a need for more and improved immunological adjuvants. The present invention satisfies this need and provides related advantages as well.

SUMMARY OF THE INVENTION

The invention provides an immunomodulatory flagellin peptide having substantially the same amino acid sequence GALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQ (SEQ ID NO:44), or a modification thereof, and having toll like receptor 5 (TLR5) binding. The immunomodulatory flagellin peptide also can have substantially the same amino acid sequence TQFSGVKVLAQDNTLTIQVGANDGETIDIDLKQINS QTLGLDTL (SEQ ID NO:45); EGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVNG (SEQ ID NO:46) or MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANF TANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQS (SEQ ID NO:47), or a modification thereof. Also provided is an immunomodulatory flagellin peptide having substantially the same amino acid sequence LQKIDAALAQVDTLRSDLGAVQNRFNSAITNL (SEQ ID NO:48), or a modification thereof, and having toll like receptor 5 (TLR5) binding. The immunomodulatory flagellin peptide also can have substantially the same amino acid sequence TLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:49) or EQAAKTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:50), or a modification thereof. Further provided is an immunomodulatory flagellin peptide having substantially the same amino acid sequence GALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAE ITQ (SEQ ID NO:44) and substantially the same amino acid sequence LQKIDAALAQVDTLRSDLGAVQNRFNSAITNL (SEQ ID NO:48), or a modification thereof, and having toll-like receptor 5 (TLR5) binding. Methods of using immunomodulatory flagellin peptides additionally are provided.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-B show NF-kB activation and TNFa production in cells expressing CD4-TLR4 or CD4-TLR5.

FIGS. 2A-B show selective induction of TLR5-stimulated activation of NF-kB by P. aeruginosa and L. monocytogenes cultures compared to LPS and lipopeptide.

FIGS. 3A-C show the purification of a TRL5-stimulating activity from L. monocytogenes culture supernatant.

FIGS. 4A-C (portions of SEQ ID NO:32 (including amino acids 1-11, amino acids 36-51, amino acids 120-134, amino acids 155-168, amino acids 224-240) and SEQ ID NO:32) show the identification by mass spectrometry of flagellin as a TLR5-stimulating activity.

FIGS. 5A-D show that flagellin expression in bacteria reconstitutes TLR5-stimulating activity.

FIG. 6 shows systemic induction of IL-6 in wild type mice treated with purified flagellin.

FIGS. 7AA-F show a comparison of flagellin amino acid sequences from 22 species of bacteria (SEQ ID NOS:11-33) and a consensus sequence of amino acid residues conserved across species (SEQ ID NO:34).

FIGS. 8A-D show that the D1 domain N- and C-terminal abrogates TLR5 recognition.

FIGS. 9A-C show that the TLR5 recognizes discrete site in the D1 domain.

FIG. 10A shows sequences in conserved regions of flagellins derived from various microorganisms. SEQ ID NOS:51-57 show sequences that occur near the N-terminus and SEQ ID NOS:58-65 show sequences derived from a region close to the C-terminus of flagellins that originate from S. typhimurium 2, S. typhimurium 1, P. aeruginosa, L. pneumophila, E. coli, S. marcescens, B. subtilis and L. monocytogenes, respectively. SEQ ID NOS:52 and 59 are specifically derived from the S. typhimurium 1 flagellin that was employed in the experiments described in Example VII herein and the complete sequence of this flagellin is SEQ ID NO:68. FIGS. 10B-10E show graphs showing that certain flagellin alanine point mutations reduce TLR5 recognition.

FIGS. 11A-F show that TLR5 recognizes monomeric rather than filamentous flagellin.

FIGS. 12A-E show that biotinylated flagellin specifically associates with TLR5.

DETAILED DESCRIPTION OF THE INVENTION

The invention is directed to flagellin derived peptides that exhibit immunomodulatory activity and to methods of inducing an immune response through activation of toll-like receptor 5 (TLR5). The identification of active flagellin peptides and their corresponding receptor, TLR5, expands the available treatment methods for inducing an immune response. Moreover, the identification of active flagellin peptides and their cognate receptor allows the identification of immunomodulatory compounds.

In one embodiment, the invention is directed to immunomodulatory flagellin peptides that bind to TLR5 and induce a TLR5-mediated activity. The peptides can be used, for example, to effectively stimulate an immune response or ameliorate a pathological condition by administration of immunomodulatory flagellin peptides and combinations of such peptides with antigens and other immunomodulatory molecules. Full length flagellin polypeptides are also used in the methods of the invention to stimulate an immune response. An advantage of the immunomodulatory flagellin peptides of the invention is that they provide the specificity of flagellin together with the availability of rapid and efficient methods for recombinant and chemical synthesis of peptides. The immunomodulatory flagellin peptides of the invention can therefore be combined with numerous well known modes of administration for the treatment of a wide variety of pathological conditions.

In another embodiment, the invention provides a method of inducing an immune response in an individual by administering a vaccine containing an immunomodulatory flagellin peptide of the invention and an antigen. An immunomodulatory flagellin peptide of the invention functions to stimulate an innate immune response. The innate immune response involves the production of immunomodulatory molecules that beneficially promote the adaptive immune response. The adaptive immune response includes both humoral and cell-mediated immune responses to antigen. Thus, a flagellin peptide functions to boost either or both humoral and cell-mediated immune responses against the antigen. A boost in an immune response causes a general increase in immune system activity that can result in the destruction of foreign or pathologically aberrant cells that otherwise could have escaped the immune response.

As used herein, the term “flagellin” is intended to mean a flagellin polypeptide contained in a variety of Gram-positive or Gram-negative bacterial species. The nucleotide and amino acid sequences of flagellin from 22 bacterial species are depicted in FIG. 7. The nucleotide sequences encoding the listed flagellin polypeptides are publically available in the NCBI Genbank database. The flagellin sequences from these and other species are intended to be encompassed by the term flagellin as used herein. Therefore, the sequence differences between species is included within the meaning of the term.

As used herein, the term “peptide” is intended to mean two or more amino acids covalently bonded together. The term “flagellin peptide” is intended to mean a peptide or fragment encoded by a portion of the nucleotide sequence or having a portion of the amino acid sequence which exhibits substantially the same sequence identity to the flagellin sequences as described above and identified in FIG. 7 and binds to toll-like receptor 5 (TLR5). For example, a flagellin peptide amino acid sequence is about 65% or greater in sequence identity to a portion of the S. Typhimurium1 sequence, GAVQNRFNSAIT, identified as SEQ ID NO:2, encoded by the nucleic acid sequence identified as SEQ ID NO:1. Therefore, flagellin peptides having amino acid substitutions that do not substantially alter TLR5 binding are included within the definition of a flagellin peptide. For example, flagellin peptides which contain one or more alanine substitutions and have substantially the same TLR5 binding activity as the flagellin peptide identified as SEQ ID NO:2 are included within the definition of a flagellin peptide. Exemplary flagellin peptides containing alanine substitutions and having substantially the same TLR5 binding activity as the flagellin peptide identified as SEQ ID NO:2 include, for example, GAVANRFNSAIT (SEQ ID NO:3) and GAVQNAFNSAIT (SEQ ID NO:4). Flagellin peptides consisting of greater than twelve amino acids and having TLR5 binding activity can similarly contain amino acid substitutions, so long as such substituted peptides retain substantially the same TLR5 binding activity. Examples of such flagellin peptides containing substitutions of various amino acid residues with alanine include ADTRDLGAVQNRFNSAIT (SEQ ID NO:37), VDARDLGAVQNRFNSAIT (SEQ ID NO:38) and VDTADLGAVQNRFNSAIT (SEQ ID NO:39). A flagellin peptide of the invention does not include a full length flagellin polypeptide. A flagellin peptide is intended to include molecules which contain, in whole or in part, non-amide linkages between amino acids, amino acid analogs and mimetics. Similarly, a flagellin peptide also includes cyclic peptides and other conformationally constrained structures. A flagellin peptide of the invention includes polypeptides having several hundred or more amino acid residues and can contain a heterologous amino acid sequence.

The term flagellin peptide specifically excludes fragments of flagellin described in Newton et al. Science, 244: 70-72 (1989); Kuwajima, G., J. Bacteriol. 170: 3305-3309 (1988); McSorley et al., J. Immunol. 164: 986-993(2000); and Samatey et al. J. Struct. Biol. 132: 106-111 (2000).

As used herein, term “immunomodulatory flagellin peptide,” is intended to mean a peptide or fragment having a portion of the amino acid sequence which exhibits substantially the same sequence identity to the flagellin sequences as described above and shown in FIG. 7 and binds to toll-like receptor 5 (TLR5). For example, an immunomodulatory flagellin peptide amino acid sequence is about 65% or greater in sequence identity to a portion of the S. Typhimurium1 sequence, GAVQNRFNSAIT, identified as SEQ ID NO:2, encoded by the nucleic acid sequence identified as SEQ ID NO:1. Therefore, immunomodulatory flagellin peptides having amino acid substitutions that do not substantially alter TLR5 binding are included within the definition of an immunomodulatory flagellin peptide. For example, immunomodulatory flagellin peptides which contain one or more alanine substitutions and have substantially the same TLR5 binding activity as the flagellin peptide identified as SEQ ID NO:2 are included within the definition of a flagellin peptide. Exemplary immunomodulatory flagellin peptides containing alanine substitutions and having substantially the same TLR5 binding activity as the flagellin peptide identified as SEQ ID NO:2 include, for example, GAVANRFNSAIT (SEQ ID NO:3) and GAVQNAFNSAIT (SEQ ID NO:4). Immunomodulatory flagellin peptides consisting of greater than twelve amino acids and having TLR5 binding activity can similarly contain amino acid substitutions, so long as such substituted peptides retain substantially the same TLR5 binding activity. Examples of such immunomodulatory flagellin peptides containing substitutions of various amino acid residues with alanine include ADTRDLGAVQNRFNSAIT (SEQ ID NO:37), VDARDLGAVQNRFNSAIT (SEQ ID NO:38) and VDTADLGAVQNRFNSAIT (SEQ ID NO:39). An immunomodulatory flagellin peptide of the invention does not include a full length flagellin polypeptide. An immunomodulatory flagellin peptide is intended to include molecules which contain, in whole or in part, non-amide linkages between amino acids, amino acid analogs and mimetics. Similarly, an immunomodulatory flagellin peptide also includes cyclic peptides and other conformationally constrained structures. An immunomodulatory flagellin peptide of the invention includes polypeptides having several hundred or more amino acid residues and can contain a heterologous amino acid sequence.

An immunomodulatory flagellin peptide, polypeptide or modification thereof, of the invention binds to toll-like receptor 5 (TLR5) and induces a TLR5-mediated response. It is understood that minor modifications can be made without destroying the TLR5 binding activity, TLR5-mediated response stimulating activity or immune response modulating activity of an flagellin peptide or polypeptide and that only a portion of the primary structure may be required in order to effect activity. Such modifications are included within the meaning of the terms flagellin polypeptide and flagellin peptide so long as TLR5 binding activity, TLR5 response stimulating or immune response stimulating activities are retained. Further, various molecules can be attached to flagellin polypeptides and peptides, including for example, other polypeptides, carbohydrates, nucleic acids or lipids. Such modifications are included within the definition of the term.

Minor modifications of flagellin polypeptide and peptides having at least about the same TLR5 binding activity, TLR5 response stimulating or immune response stimulating activity as the referenced polypeptide or peptide include, for example, conservative substitutions of naturally occurring amino acids and as well as structural alterations which incorporate non-naturally occurring amino acids, amino acid analogs and functional mimetics. For example, a Lysine (Lys) is considered to be a conservative substitution for the amino acid Arg. Similarly, a flagellin peptide containing mimetic structures having similar charge and spacial arrangements as reference amino acid residues would be considered a modification of the reference polypeptide or peptide so long as the peptide mimetic exhibits at least about the same activity as the reference peptide.

As used herein, the term “amino acid” is intended to mean both naturally occurring and non-naturally occurring amino acids as well as amino acid analogs and mimetics. Naturally occurring amino acids include the 20 (L)-amino acids utilized during protein biosynthesis as well as others such as 4-hydroxyproline, hydroxylysine, desmosine, isodesmosine, homocysteine, citrulline and ornithine, for example. Non-naturally occurring amino acids include, for example, (D)-amino acids, norleucine, norvaline, p-fluorophenylalanine, ethionine and the like. Amino acid analogs include modified forms of naturally and non-naturally occurring amino acids. Such modifications can include, for example, substitution or replacement of chemical groups and moieties on the amino acid or by derivitization of the amino acid. Amino acid mimetics include, for example, organic structures which exhibit functionally similar properties such as charge and charge spacing characteristic of the reference amino acid. For example, an organic structure which mimics Arginine (Arg or R) would have a positive charge moiety located in similar molecular space and having the same degree of mobility as the e-amino group of the side chain of the naturally occurring Arg amino acid. Mimetics also include constrained structures so as to maintain optimal spacing and charge interactions of the amino acid or of the amino acid functional groups. Those skilled in the art know or can determine what structures constitute functionally equivalent amino acid analogs and amino acid mimetics.

Specific examples of amino acid analogs and mimetics can be found described in, for example, Roberts and Vellaccio, The Peptides: Analysis, Synthesis, Biology, Eds. Gross and Meinhofer, Vol. 5, p. 341, Academic Press, Inc., New York, N.Y. (1983), the entire volume of which is incorporated herein by reference. Other examples include peralkylated amino acids, particularly permethylated amino acids. See, for example, Combinatorial Chemistry, Eds. Wilson and Czarnik, Ch. 11, p. 235, John Wiley & Sons Inc., New York, N.Y. (1997), the entire book of which is incorporated herein by reference. Yet other examples include amino acids whose amide portion (and, therefore, the amide backbone of the resulting peptide) has been replaced, for example, by a sugar ring, steroid, benzodiazepine or carbo cycle. See, for instance, Burger's Medicinal Chemistry and Drug Discovery, Ed. Manfred E. Wolff, Ch. 15, pp. 619-620, John Wiley & Sons Inc., New York, N.Y. (1995), the entire book of which is incorporated herein by reference. Methods for synthesizing peptides, polypeptides, peptidomimetics and proteins are well known in the art (see, for example, U.S. Pat. No. 5,420,109; M. Bodanzsky, Principles of Peptide Synthesis (1st ed. & 2d rev. ed.), Springer-Verlag, New York, N.Y. (1984 & 1993), see Chapter 7; Stewart and Young, Solid Phase Peptide Synthesis, (2d ed.), Pierce Chemical Co., Rockford, Ill. (1984), each of which is incorporated herein by reference).

As used herein, the term “immune response” is intended to mean to a measurable or observable reaction to an antigen or immunomodulatory molecule mediated by one or more cells of the immune system. An immune response begins with an antigen or immunomodulatory molecule binding to an immune system cell and terminates with destruction of antigen and cells containing antigen or alteration in immune cell function. A reaction to an antigen or immunomodulatory molecule is mediated by many cell types, including a cell that initially binds to an antigen or immunomodulatory molecule and cells that participate in mediating an innate, humoral, cell-mediated immune response. An innate immune response involves binding of pathogen-associated molecular patterns (PAMPs) to cell surface receptors, such as toll-like receptors. Activation of toll-like receptors in response to PAMPs leads to the production of immunomodulatory molecules, such as cytokines and co-stimulatory molecules, that induce an immune response. A humoral response involves interaction of B cells with antigen and B cell differentiation into antibody-secreting cells. A cell-mediated response involves various subpopulations of T cells that recognize antigen presented on self-cells, including helper T cells that respond to antigen by producing cytokines and cytotoxic T cells that respond to antigen by developing into cytotoxic T lymphocytes, which mediate killing of altered self-cells. The term immune response includes measurable or observable reactions produced by any cell type that participates in the processes through which immune system cells are activated and antigen containing cells are destroyed. Such measurable reactions include, for example, production of immunomodulatory molecules, migration and proliferation.

An “immunomodulatory molecule” is a molecule that alters an immune response. An immunomodulatory molecule can be, for example, a compound, such as an organic chemical; a polypeptide, such as an antibody or cytokine; a nucleic acid, such as a DNA or RNA molecule; or any other type of molecule that alters an immune response. An immunomodulatory molecule can alter an immune response by directly or indirectly altering an activity of a cell that mediates an immune response. An immunomodulatory molecule can act directly on an immune system cell, for example, by binding to a cell surface receptor and stimulating or inhibiting proliferation, differentiation, or expression, secretion or receptor binding of immune system regulatory molecules such as co-stimulatory receptors and ligands, cytokines, and chemokines. Examples of naturally occurring molecules that act directly on immune system cells to alter an immune response include PAMPs, cytokines, chemokines and growth factors. Other examples of molecules that act directly on immune system cells to alter an immune response include molecules that alter receptor functions, such as antibodies to receptors, soluble cytokine receptors, receptor agonists and antagonists, molecules that alter the production of immunomodulatory molecules, such as inhibitors of converting enzymes and molecules involved in the intracellular transport and secretion of immunomodulatory molecules.

An immunomodulatory molecule can indirectly alter the activity of a particular immune system cell by altering the amount or activity of a molecule that regulates a cellular activity of the cell. For example, a cytokine, chemokine, or growth factor produced by an immune system cell, such as a macrophage, can stimulate or inhibit various cellular activities of B and T lymphocytes. Immune cell functions that can be stimulated or inhibited by an immunomodulatory molecule include, for example, immune cell activation, co-activation, proliferation, production of cytokines, cellular interactions and migration. An immunomodulatory molecule can therefore act on a variety of immune cell types and can alter a variety of cellular functions. An immunomodulatory flagellin peptide, polypeptide or modifications thereof used in the methods of the invention are examples of immunomodulatory molecules useful for inducing an immune response, for example, by binding to TLR5 and inducing a TLR5-mediated increase in macrophage production of TNFa, IL-1 and IL-6. The flagellin polypeptides, peptides and modifications thereof, are also useful for indirectly inducing an immune response because immunomodulatory molecules produced by a TLR5-expressing cell in response to flagellin will alter the activities of immune system cells that respond to the particular immunomodulatory molecules produced.

An immunomodulatory molecule can mediate an immune response that is specific for a target antigen or nonspecific. A specific immunomodulatory molecule alters an immune response to a particular target antigen. Examples of specific immunomodulatory molecules include monoclonal antibodies, including naked monoclonal antibodies, drug-, toxin- or radioactive compound-conjugated monoclonal antibodies, and ADCC targeting molecules. Such immunomodulatory molecules stimulate an immune response by binding to antigens and targeting cells for destruction. An immunomodulatory molecule can be used to suppress an immune response to an antigen. For example, a tolerogenizing molecule can be used to suppress an immune response to a self-antigen.

Nonspecific immunomodulatory molecules stimulate or inhibit the immune system in a general manner through various mechanisms that can include, for example, stimulating or suppressing cellular activities of immune system cells. Nonspecific immunomodulatory molecules useful for stimulating an immune responses include, for example, agents that stimulate immune cell proliferation, immune cell activation and production of cytokines and co-stimulatory molecules. Well known immunomodulatory molecules that stimulate an immune response are, for example, interleukins, interferons, levamisole and keyhole limpet hemocyanin. Nonspecific immunomodulatory molecules useful for suppressing immune responses include, for example, agents that inhibit cytokines synthesis or processing, specific cytokine receptor blocking reagents such as soluble receptors and receptor antagonists, and cytokines that down-regulate or inhibit the production of other immunomodulatory molecules. Well known immunomodulatory molecules for suppressing an immune response include, for example, cyclosporin, rapamycin, tacrolimus, azathioprine, cyclophosphamide and methotrexate.

Immunomodulatory molecules can be contained in a mixture of molecules, including a natural or man-made composition of molecules. Exemplary natural compositions of immunomodulatory compounds include, for example, those contained in an organism such as Bacille Calmette-Guerin (BCM) or Corynbacterium parvum. Exemplary man-made compositions of immunomodulatory molecules include, for example, QS-21, DETOX and incomplete Freund's adjuvant.

As used herein, the term “adjuvant” when used in reference to a vaccine, is intended to mean a substance that acts generally to accelerate, prolong, or enhance the quality of specific immune responses to a vaccine antigen. An adjuvant can advantageously reduce the number of immunizations or the amount of antigen required for protective immunization.

As used herein, the term “antigen-specific immune response” is intended to mean a reaction of one or more cells of the immune system to a particular antigen that is not substantially cross-reactive with other antigens.

As used herein, the term “antigen” is intended to mean a molecule which induces an immune response. An antigen can be a crude mixture of molecules, such as a cell, or one or more isolated molecules. Examples of crude antigens include attenuated organisms, inactivated organisms, viral particles and tumor cells. Examples of isolated antigens include a polypeptide, lipoprotein, glycoprotein, lipid, anti-idiotype antibody, toxoid, polysaccharide, capsular polysaccharide and nucleic acid. Such isolated antigens can be naturally occurring, recombinantly produced, or synthesized. Exemplary naturally occurring antigens include purified microbial macromolecules. Exemplary recombinantly produced antigens include cloned microbial and tumor cell antigens. Exemplary synthesized antigens include synthetic peptides and nucleic acids.

As used herein, the term “vaccine” is intended to mean a compound or formulation which, when administered to an individual, stimulates an immune response against an antigen. A vaccine is useful for preventing or ameliorating a pathological condition that will respond favorably to immune response modulation. A vaccine can contain isolated or crude antigen, and can contain one or more antigens. A vaccine can contain one or more adjuvants.

As used herein, the term “immunogenic amount” is intended to mean an amount of an immunomodulatory flagellin polypeptide, peptide or modifications thereof, or combinations thereof with one or more molecules, such as an antigen or other immunomodulatory molecule, required to effect an immune response. The dosage of an immunomodulatory flagellin polypeptide, peptide, or modifications thereof, independently or in combination with one or more molecules, will depend, for example, on the pathological condition to be treated, the weight and condition of the individual and previous or concurrent therapies. The appropriate amount considered to be an immunogenic dose for a particular application of the method can be determined by those skilled in the art, using the guidance provided herein. For example, the amount can be extrapolated from in vitro or in vivo assays as described below. Those skilled in the art will understand that the condition of the patient needs to be monitored through the course of therapy and that the amount of the composition that is administered can be adjusted according to patient response to therapy.

The term “pathologically aberrant cell” is intended to mean a cell that is altered from a normal physiological or cellular state. Such alteration can be due to changes in physiology or phenotype associated with a disease or abnormal condition of a mammalian cell or tissue. Pathologically aberrant cells include cells lacking normal control of cellular functions, such as growth, differentiation, and apoptosis, resulting in altered gene and protein expression. Cells that lack normal growth control proliferate in the absence of appropriate growth signals, resulting in damage in structure or function of surrounding tissues. Cells that lack normal differentiation undergo inappropriate phenotypic or physiological changes that do not normally characterize the cell type, resulting in damage in structure and function or surrounding tissues. Cells that lack normal apoptosis fail to undergo, or inappropriately undergo the process of cell death, resulting in damage in structure or function of surrounding tissues. Altered protein expression is an example of a phenotype change that renders such cells distinguishable from normal. For example, increased or decreased expression of a polypeptide normally expressed on a cell, expression of a mutated polypeptide and expression of a polypeptide not normally expressed on a cell are phenotypic changes that can alter a cell from normal. Examples of pathologically aberrant cells include tumor cells and degenerating cells.

As used herein, the term “pathological condition” is intended to mean a disease, abnormal condition or injury of a mammalian cell or tissue. Such pathological conditions include, for example, hyperproliferative and unregulated neoplastic cell growth, degenerative conditions, inflammatory diseases, autoimmune diseases and infectious diseases. Pathological conditions characterized by excessive or unregulated cell growth include, for example, hyperplasia, cancer, autoimmune disease and infectious disease. Hyperplastic and cancer cells proliferate in an unregulated manner, causing destruction of tissues and organs. Specific examples of hyperplasias include benign prostatic hyperplasia and endometrial hyperplasia. Specific examples of cancer include prostate, breast, ovary, lung, uterus, brain and skin cancers. Abnormal cellular growth can also result from infectious diseases in which foreign organisms cause excessive growth. For example, human papilloma viruses can cause abnormal growth of skin cells. The growth of cells infected by a pathogen is abnormal due to the alteration of the normal condition of a cell resulting from the presence of a foreign organism. Specific examples of infectious diseases include DNA and RNA viral diseases, bacterial diseases, parasitic diseases. Similarly, the growth of cells mediating autoimmune and inflammatory diseases are aberrantly regulated which results in, for example, the continued proliferation and activation of immune mechanisms with the destruction of tissues and organs. Specific examples of autoimmune diseases include, for example, rheumatoid arthritis and systemic lupus erythmatosis. Specific examples of degenerative disease include osteoarthritis and Alzheimer's disease.

By specific mention of the above categories of pathological conditions, those skilled in the art will understand that such terms include all classes and types of these pathological conditions. For example, the term cancer is intended to include all known cancers, whether characterized as malignant, benign, soft tissue or solid tumor. Similarly, the terms infectious diseases, degenerative diseases, autoimmune diseases and inflammatory diseases are intended to include all classes and types of these pathological conditions. Those skilled in the art will know the various classes and types of proliferative, infectious, autoimmune and inflammatory diseases.

As used herein the term “toll-like receptor 5” or “TLR5” is intended to mean a toll-like receptor 5 of any species, such as the murine and human polypeptides containing the amino acid sequences set forth as SEQ ID NOS:6 and 8, respectively, encoded by the nucleic acid sequence identified as SEQ ID NOS:5 and 7, respectively. A TLR5 is activated upon binding to flagellin, an immunomodulatory flagellin peptide, or modifications thereof, and other TLR5 agonists. Upon activation, a TLR5 induces a cellular response by transducing an intracellular signal that is propagated through a series of signaling molecules from the cell surface to the nucleus. For example, the intracellular domain of TLR5 recruits an adaptor protein, MyD88, which recruits the serine kinase IRAK. IRAK forms a complex with TRAF6, which then interacts with various molecules that participate in transducing the TLR signal. These molecules and other TRL5 signal transduction pathway components stimulate the activity of transcription factors, such as fos, jun and NF-kB, and the corresponding induction of gene products of fos-, jun- and NF-kB-regulated genes, such as, for example, TNFa, IL-1 and IL-6. The activities of signaling molecules that mediate the TLR5 signal, as well as molecules produced as a result of TLR5 activation are TLR5 activities that can be observed or measured. Therefore, a TLR5 activity includes binding to a flagellin polypeptide, immunomodulatory flagellin peptide, or a modification thereof, recuitment of intracellular signaling molecules, as well as downstream events resulting from TLR5 activation, such as transcription factor activation and production of immunomodulatory molecules. A TLR5 cellular response mediates an innate immune system response in an animal because cytokines released by TLR5-expressing cells regulate other immune system cells to promote an immune response in an animal. Therefore, as used herein the term “TLR5-mediated response” is intended to mean the ability of a flagellin polypeptide, immunomodulatory peptide or modification thereof to induce a TLR5-mediated cellular response. Exemplary TLR5-mediated cellular responses include activation of transcription factors such as fos, jun and NF-kB, production of cytokines such as IL-1, IL-6 and TNFa, and the stimulation of an immune response in an animal.

A TLR5 also encompasses polypeptides containing minor modifications of a native TLR5, and fragments of a full-length native TLR5, so long as the modified polypeptide or fragment retains one or more biological activities of a native TLR5, such as the abilities to stimulate NF-kB activity, stimulate the production of cytokines such as TNFa, IL-1, and IL-6 and stimulate an immune response in response to TLR5 binding to flagellin polypeptide, immunomodulatory peptide or modifications thereof. A modification of a TLR5 can include additions, deletions, or substitutions of amino acids, so long as a biological activity of a native TLR5 is retained. For example, a modification can serve to alter the stability or activity the polypeptide, or to facilitate its purification. Modifications of polypeptides as described above in reference to flagellin polypeptides and peptides are applicable to TLR5 polypeptides of the invention. A “fragment” of a TLR5 is intended to mean a portion of a TLR5 that retains at least about the same activity as a native TLR5.

As used herein, the term “TLR5 agonist” refers to a compound that selectively activates or increases normal signal transduction through TLR5. As used herein, the term “TLR5 antagonist” refers to a compound that selectively inhibits or decreases normal signal transduction through TLR5. A TLR5 agonist or antagonist can alter normal signal transduction through TLR5 indirectly, for example, by modifying or altering the native conformation of TLR5 or a TLR5 ligand. For therapeutic applications, a TLR5 agonist or antagonist has an EC50 of less than about 10⁻⁷ M, such as less than 10⁻⁸ M and less than 10⁻⁹ M, although a TRL5 agonist with a higher EC50 can be therapeutically useful. As used herein, the term “TLR5 ligand” refers to a compound that binds a TLR5 polypeptide with high affinity. A TLR5 ligand can further be an agonist or antagonist of TLR5, as described above, or can be a compound having little or no effect on TLR5 signaling.

As used herein, the term “detectably labeled” refers to derivitization with, or conjugation to, a moiety that is detectable by an analytical or qualitative method. A detectable moiety can be, for example, a radioisotope, such as ¹⁴C, ¹³¹I, ³²P or ³H, fluorochrome, ferromagnetic substance, or luminescent substance.

As used herein the term “ADCC targeting molecule” is intended to mean

an antigen binding protein containing a Fc receptor binding domain capable of inducing antibody-dependent cell cytotoxicity (ADCC). An ADCC targeting molecule can also contain other domains that augment induction of ADCC. The flagellin polypeptides and peptides, immunomodulatory peptides, and modifications described herein, can be domains of an ADCC targeting molecule that augment induction of ADCC. The ADCC targeting molecule can include multiple valencies for either or both the antigen binding domain or the Fc receptor binding domain. Additionally, an ADCC targeting molecule also can have multiple different antigen binding domains combined with a single or multiple copies of an Fc receptor binding domain or combined with different Fc receptor binding domains. The antigen binding domain or domains can be derived from essentially any molecule that has selective or specific binding activity to a target antigen so long as it can be fused or attached to one or more Fc receptor binding domains while still maintaining antigen binding activity. The Fc receptor binding domain can be derived from an antibody constant region of, for example, the IgG class, including subclasses IgG1, IgG3 and IgG4. Such Fc receptor binding domains can be used in their native form or the amino acid sequence can be modified so as to enhance or optimize the Fc receptor binding or ADCC activity. Moreover, the Fc receptor binding domains can be derived from constant regions which recognize either stimulatory or inhibitory Fc receptors. The Fc receptor binding domain is located within the hinge region of an antibody constant region where the cognate receptors bound by this domain include, for example, the Fc RI, Fc RIIA and Fc RIII. Therefore, ADCC targeting molecules include, for example, antibodies selective for a target antigen and functional variants thereof as well as fusion proteins and chemical conjugates containing both an antigen binding domain and a Fc receptor binding domain in functionally active forms. ADCC targeting molecules and the use of ADCC targeting molecules in the treatment of disease are described in detail in U.S. patent application Ser. No. 09/618,176, which is incorporated herein by reference.

The term “about” when used in reference to a particular activity or measurement is intended to refer to the referenced activity or measurement as being within a range values encompassing the referenced value and within accepted standards of a credible assay within the art, or within accepted statistical variance of a credible assay within the art.

As used herein, the term “substantially” or “substantially the same” when used in reference to an amino acid sequence is intended to mean that the amino acid sequence shows a considerable degree, amount or extent of sequence identity when compared to the reference sequence. Such considerable degree, amount or extent of identity is further considered to be significant and meaningful and therefore exhibit characteristics which are definitively recognizable or known as being derived from or related to flagellin. For example, an amino acid sequence which is substantially the same amino acid sequence as an flagellin peptide, including fragments thereof, refers to a sequence which exhibits characteristics that are definitively known or recognizable as being sufficiently related to flagellin so as to fall within the classification of flagellin sequences as defined above. Minor modifications thereof are included so long as they are recognizable as an flagellin sequence as defined above.

As used herein, the term “individual” is intended to mean any animal in which an immune response can be induced by a flagellin polypeptide, peptide or modifications thereof including a human, non-human primate, cow, pig, chicken, rabbit, ferret, rat or mouse.

An immunomodulatory flagellin polypeptide, peptide or modifications thereof can be used to induce an immune response in an individual having a pathological condition, promoting the individual's own immune system to function more effectively and thereby ameliorate the pathological condition. An individual's immune system may not recognize cancer cells and other types of pathologically aberrant cells as foreign because the particular antigens are not different enough from those of normal cells to cause an immune reaction. In addition, the immune system may recognize cancer cells, but induce a response insufficient to destroy the cancer. By stimulating an innate immune response, immunomodulatory flagellin peptide, polypeptide or modification thereof, promote humoral and cell-mediated responses to antigens on foreign cells or pathologically aberrant cells, such as cancer cells. Administered independently or in combination with an antigen, such as a tumor antigen, a flagellin polypeptide, peptide or modification thereof, can be used to boost the immune system's recognition of cancer cells and other pathologically aberrant cells, and target such cells for destruction.

Flagellin is a pathogen-associated molecular pattern (PAMP) recognized by toll-like receptor 5 (TRL5). Toll-like receptor 5 is a member of a family of at least 10 receptors involved in mediated the innate immune response. Toll-like receptors recognize PAMPs that distinguish infectious agents from self and mediating the production of immunomodulatory molecules, such as cytokines, necessary for the development of effective adaptive immunity (Aderem, A and Ulevitch, R. J. Nature 406: 782-787 (2000) and Brightbill, H. D., Immunology 101: 1-10 (2000)). Members of the toll-like receptor family recognize a variety of antigen types and can discriminate between pathogens. For example, TLR2 recognizes various fungal, Gram-positive, and mycobacterial components, TLR4 recognizes the Gram-negative product lipopolysaccharide (LPS), and TLR9 recognizes nucleic acids such as CpG repeats in bacterial DNA. TLR5 has now been identified as a receptor for bacterial flagellin.

Flagellin induces an innate immune response by binding to and activating TLR5. Activation of TLR5 by binding to flagellin induces the production of immunomodulatory molecules, such as cytokines and co-stimulatory molecules, by a TLR5-expressing cell. For example, activation of TLR5 in macrophages results in the expression of the cytokines TNFα, IL-1 and IL-6. These cytokines directly and indirectly alter the activities of immune system cells that participate in both humoral (TH2) and cell-mediated (TH1) adaptive immune responses. In this manner, an immunomodulatory flagellin peptide, polypeptide or modification thereof, acts as an adjuvant to stimulate a general immune response.

Altering the balance of TH1-versus TH2-associated cytokines can be used to favorably alter an immune response to treat certain diseases. For example, in the use of cancer vaccines, it can be favorable to induce both TH1 and TH2 responses (Herlyn and Birebent, Ann. Med., 31: 66-78, (1999)). Different sets of cytokines orchestrate TH1 and TH2 immune responses. For example, TH1 immune responses are associated with the cytokines IL-2, IFN-g, and TNFα while TH2 immune responses are associated with the cytokines IL-4, IL-5, IL-6 and IL-10. TLR5 stimulates the production of cytokines associated with both TH1- and TH2-associated cytokines. For example, TNFa is associated with the stimulation of a TH1 type immune response (Ahlers, J D et al. J. Immunol, 158: 3947-58 (1997)), and IL-6 is associated with the stimulation of a TH2 type response (Steidler, L. et al. Infect. Immun., 66: 3183-9, (1998)). Therefore, an immunomodulatory flagellin peptide, polypeptide or modification thereof, can be used to advantageously elicit TH1 and TH2 type immune responses.

An immunomodulatory flagellin peptide, polypeptide or modification thereof can also be used to generally alter the particular cytokines involved in an immune response in an individual. Alterations from normal levels of cytokines are observed in many disease states. For this reason, it can be desirable to increase or decrease the amounts or activities of specific cytokines involved in particular pathological conditions. The cytokines produced in response to TLR5 activation can both stimulate and down-regulate the production of other cytokines. Therefore, an immunomodulatory flagellin peptide, polypeptide or modification thereof, or combination of a flagellin molecule with an immunomodulatory molecule or antigen can be used to alter levels of cytokines associated with a pathological condition. For example, an immunomodulatory flagellin peptide can increase TLR5-expressing macrophage production of TNFa, IL-1 and IL-6. TNFa and IL-1 generally function as pro-inflammatory cytokines. IL-6 generally functions as an anti-inflammatory cytokine and induces a variety of anti-inflammatory activities in immune system cells. For example, IL-6 stimulates the production of many anti-inflammatory anti-proteases. Those skilled in the art will be able to determine if a pathological condition in an individual could be ameliorated by inducing TLR5-stimulated cytokine production and will be able to determine appropriate combinations of flagellin and immunomodulatory molecules suitable for inducing a beneficial immune response.

The invention provides an immunomodulatory flagellin peptide comprising at least about 10 amino acids of substantially the amino acid sequence GAVQNRFNSAIT (SEQ ID NO:2), or a modification thereof, that binds to toll-like receptor 5 (TLR5).

The flagellin peptide identified by SEQ ID NO:2 is a peptide of S. Typhimurium1 flagellin which is encoded by the nucleic acid sequence identified by SEQ ID NO:1. A flagellin peptide of the invention also includes peptides from other bacterial species, such as H. Pylori (SEQ ID NO:12), V. Cholera (SEQ ID NO:13), S. marcesens (SEQ ID NO:20), S. flexneri (SEQ ID NO:22), T. Pallidum (SEQ ID NO:23 or SEQ ID NO:24), L. pneumophila (SEQ ID NO:25), B. burgdorferei (SEQ ID NO:26), C. difficile (SEQ ID NO:28), R. meliloti (SEQ ID NO:29), A. tumefaciens (SEQ ID NO:30), R. lupini (SEQ ID NO:31), B. clarridgeiae (SEQ ID NO:33), P. Mirabilis (SEQ ID NO:16), B. subtilus (SEQ ID NO:27), L. monocytogenes (SEQ ID NO:32), P. aeruginosa (SEQ ID NO:14) and E. coli (SEQ ID NO:21), which contain amino acid sequences having 21-71% identity over the 12 amino acid sequence of SEQ ID NO:2. A flagellin peptide of the invention also includes flagellin peptides from other bacterial species, including peptides contained within the flagellin amino acid sequences shown FIG. 7 (SEQ ID NOS:11-34). Thus, a flagellin peptide of the invention can have greater than about 65% identity, such as greater than about 75%, greater than about 85%, greater than about 95%, greater than about 98% identity with the peptide identified by SEQ ID NO:2.

A flagellin peptide of the invention is derived from a conserved region of a flagellin polypeptide. Conserved regions of flagellin are well known in the art and have been described, for example, in Mimori-Kiyosue, et al., J. Mol. Viol. 270: 222-237, (1997). Whereas T cell receptors which mediate the adaptive immune response recognize random portions of antigen amino acid sequences, toll-like receptors recognize conserved portions of antigen amino acid sequences. Therefore, the flagellin peptides of the invention and immunomodulatory flagellin peptides used in the methods of the invention contain amino acid sequences derived from conserved regions of flagellin.

The invention also provides an immunomodulatory flagellin peptide located in the D1 region of the flagellin polypeptide. The immunomodulatory flagellin peptide includes substantially the same sequence as GALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQ (SEQ ID NO:44), or a modification thereof, and has toll like receptor 5 (TLR5) binding. This immunomodulatory flagellin peptide is described further below in Example VII and corresponds to amino acid residues 79-117 of flagellin polypeptide with reference to the S. Typhimurium 1 amino acid sequence. A schematic of the three dimensional structure of flagellin polypeptide and its corresponding domains D1, D2 and D3 are shown in FIG. 8. FIG. 10 shows an alignment of SEQ ID NO:44 with flagellin peptides from this same amino terminal D1 region identified from other species of flagellin polypeptides (SEQ ID NOS:51-57).

Other immunomodulatory flagellin peptides located in the amino terminal D1 region of flagellin polypeptide include substantially the same amino acid sequence TQFSGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTL (SEQ ID NO:45), corresponding to amino acid residues 129-172 of flagellin; EGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVNG (SEQ ID NO:46) corresponding to amino acid residues 78-127 of flagellin or MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANF TANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQS (SEQ ID NO:47), corresponding to amino acid residues 0-98 of flagellin, or a modification thereof, where the amino acid residue denoted as “0” corresponds to the initial methonine residue shown in the flagellin sequences in FIG. 7 (and denoted as amino acid residue 1 therein).

The invention also provides and an immunomodulatory flagellin peptide located in the D1 region of the flagellin polypeptide and corresponding to the carboxyl terminal portion of a flagellin polypeptide. The immunomodulatory flagellin peptide includes substantially the same amino acid sequence as LQKIDAALAQVDTLRSDLGAVQNRFNSAITNL (SEQ ID NO:48), or a modification thereof, and has toll like receptor 5 (TLR5) binding. This immunomodulatory flagellin peptide is described further below in Example VII and corresponds to amino acid residues 408-439 of flagellin polypeptide with reference to S. Typhimurium 1 amino acid sequence. A schematic of the three dimensional structure of flagellin polypeptide and its corresponding domains D1, D2 and D3 are shown in FIG. 8. FIG. 10 shows an alignment of SEQ ID NO:48 with flagellin peptides from this same carboxyl terminal D1 region identified from other species of flagellin polypeptides (SEQ ID NOS:58-65).

Other immunomodulatory flagellin peptides located in the carboxyl terminal D1 region of flagellin polypeptide include substantially the same amino acid sequence as TLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:49), corresponding to amino acid residues 420-448 of flagellin or EQAAKTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:50), corresponding to amino acid residues 398-448 of flagellin, or a modification thereof.

Exemplary modifications of the D1 derived immunomodulatory flagellin peptides are shown in FIGS. 8-10. Those immunomodulatory flagellin peptides having modifications that do not substantially affect TLR5 binding or TLR5 stimulating activity are included within the modified flagellin peptides of the invention.

Also provided are immunomodulatory flagellin peptides containing the above D1 region flagellin peptides or modifications thereof that are absent some or all of the flagellin polypeptide D2 and/or D3 region sequence. Such single chain D1 immunomodulatory flagellin peptides combine active non-contiguous portions of the amino terminal D1 and the carboxyl terminal D1 regions into a contiguous peptide sequence. Single chain D1 immunomodulatory flagellin peptides can be produced by, for example, deletion of some or all of the D2 or D3 domains or alternatively, the amino terminal D1 region and the carboxyl terminal D1 region sequences can be combined using a linker or other moiety that attaches these domains. Attachment can be through chemical linking of the peptides or by recombinant methodology through expression of a single chain encoding nucleic acid. All of such methods are well known to those skilled in the art. Single chain D1 immunomodulatory flagellin peptides can include any one of the amino terminal peptides described previous as SEQ ID NOS:44-47 and 51-57 linked in combination with any one of the carboxyl terminal peptides described previously as SEQ ID NOS:48-50 and 58-65. Immunomodulatory flagellin peptides corresponding to SEQ ID NOS:44-65 derived from other species similarly can be used in a single chain D1 immunomodulatory flagellin peptide of the invention.

As shown in FIGS. 8 and 9, the amino and carboxyl terminal portions of a flagellin polypeptide corresponding to the D1 region associate with each other by affinity interactions. Similarly, the amino and carboxyl terminal components of the single chain D1 immunomodulatory flagellin peptides of the invention also will associate with each other to mimic the interactions of these domains in a flagellin polypeptide. Methods for constructing active single chain molecules from such interacting domains are well known to those skilled in the art.

Therefore, the invention provides an immunomodulatory flagellin peptide having substantially the same amino acid sequence as GALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAE ITQ (SEQ ID NO:44) and substantially the same amino acid sequence as LQKIDAALAQVDTLRSDLGAVQNRFNSAITNL (SEQ ID NO:48), or a modification thereof, and having toll like receptor 5 (TLR5) binding. Single chain D1 immunomodulatory flagellin peptides also can have any one of substantially the same amino acid sequence as TQFSGVKVLAQDNTLTIQVGANDGETIDIDLKQINS QTLGLDTL (SEQ ID NO:45); EGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVNG (SEQ ID NO:46) or MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANF TANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQS (SEQ ID NO:47), and have any one of substantially the same amino acid sequence as TLRSDLGAVQNRFNSAITNLG NTVNNLSS (SEQ ID NO:49) or EQAAKTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSS (SEQ ID NO:50), or a modification thereof.

A flagellin peptide of the invention excludes a portion of flagellin described in Newton et al. (supra, 1989), which consists of an S. meunchen flagellin fragment containing a deletion of amino acids 207-223, portions of E. coli (strain K12) flagellin described in Kuwaijima et al. (supra, 1998), which consist of E. coli flagellin fragments containing deletions of amino acids 239-254, 259-278, 237-262, 194-379, 201-318, 218-326, 211-347, 210-299, 245-301, and 220-299, a portion of flagellin described in Samatey et al. (supra, 2000), which consists of an S. typhimurium flagellin fragment lacking 52 N-terminal amino acid residues and lacking 44 C-terminal amino acid residues, and portions of flagellin described in McSorley et al. (supra, 2000) which consist of S. typhimurium flagellin fragments having the following amino acid sequences: RSDLGAVQNRFNSAI (SEQ ID NO:40), DLGAVQNRFNSAITN (SEQ ID NO:41), GAVQNRFNSAITNLG (SEQ ID NO:42) AND VQNRFNSAITNLGNT (SEQ ID NO:43).

An immunomodulatory flagellin peptide of the invention can contain a heterologous amino acid sequence that imparts structural or functional characteristics onto the flagellin peptide. For example, chimeric flagellin peptides or modifications can be used to impart a targeting function. Targeting of a flagellin peptide or modification to a particular site, such as a mucosal surface for example, confers additional therapeutic advantage of inducing an immune response at a site of pathological condition or a site favored for inducing an antigen-specific immune response, for example by a vaccine. Further, chimeric flagellin peptides can include a sequence that facilitates detection, purification or enhances immunomodulatory activity of the flagellin peptide. A flagellin peptide can be contained, for example, in an ADCC targeting molecule used to treat a pathological condition. A flagellin peptide can augment the effectiveness of an ADCC targeting molecule by, for example, stimulating an innate immune response through TLR5, such as the induction of cytokines such as TNFa, IL-1 and IL-6. Similarly, a flagellin peptide can contain amino acid sequences of a variety of antigen polypeptides, such as those described above in reference to antigens contained in vaccines used in the methods of the invention. A chimeric flagellin peptide containing amino acid sequences of an antigen or containing an antigenic molecule such as a carbohydrate, nucleic acid, or lipid, can be used analogously to a vaccine, as described above, as well as in a vaccine formulation, to induce an immune response in an individual. As such, a chimeric flagellin peptide can be a vaccine that induces both innate and adaptive immune system responses.

An immunomodulatory flagellin peptide of the invention can be prepared by a variety of methods well-known in the art, for example, by recombinant expression systems described below, and biochemical purification methods described below, as well as by synthetic methods well known in the art. Methods for recombinant expression and purification of polypeptides in various host organisms are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1992) and in Ansubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1998), both of which are incorporated herein by reference. Similarly, flagellin peptide modifications can be generated using recombinant mutagenesis, such as site directed mutagenesis and PCR mutagenesis, and expression of the flagellin peptide modification. Numerous methods of constructing, modifying, expressing and purifying peptides are known to those skilled in the art. A specific example of a method for purifying flagellin is described below in Example III. The choice of recombinant methods, expression and purification systems will be known by those skilled in the art and will depend on the user and the particular application for the immunomodulatory flagellin peptide or modification thereof.

A flagellin peptide of the invention induces an innate immune response in an individual by binding to an stimulating TLR5. Therefore, the invention provides methods for inducing an immune response in an individual having a pathological condition that can be ameliorated by immune system activity. The methods involve administering an immunomodulatory flagellin peptide or modification thereof to induce an immune response, administering a combination of an immunomodulatory flagellin peptide and an antigen to induce an antigen-specific immune response, and administering a combination of an immunomodulatory flagellin peptide and an immunomodulatory molecule to modulate an immune response. The selection of a particular method for inducing an immune response will depend on the particular pathological condition to be ameliorated or prevented in an individual. As described herein, the methods are applicable to a wide variety of pathological conditions. Those skilled in the art will be able to determine if an immune response can be beneficially modulated by administering an immunomodulatory flagellin peptide or combination thereof with an antigen or immunomodulatory molecule.

The invention provides method of inducing an antigen-specific immune response in an individual. The method involves administering to an individual an immunogenic amount of a vaccine, comprising an antigen and an immunomodulatory flagellin peptide having at least about 10 amino acids of substantially the amino acid sequence of SEQ ID NO:2, or a modification thereof.

As an adjuvant in a vaccine formulation, the immunomodulatory flagellin peptides of the invention can contribute to the effectiveness of the vaccine by, for example, enhancing the immunogenicity of weaker antigens such as highly purified or recombinant antigens, reducing the amount of antigen required for an immune response, reducing the frequency of immunization required to provide protective immunity, improve the efficacy of vaccines in individuals with reduced or weakened immune responses, such as newborns, the aged, and immunocompromised individuals, and enhance the immunity at a target tissue, such as mucosal immunity, or promote cell-mediated or humoral immunity by eliciting a particular cytokine profile. An immunomodulatory flagellin peptide, polypeptide or modification thereof induces an innate immune response through activation of TLR5. The innate immune response increases the immune response to an antigen by stimulating the adaptive immune response. Therefore, a combination of an immunomodulatory flagellin peptide, polypeptide or modification thereof with one or more antigens provides an effective vaccine for inducing an immune response in an individual.

The methods of the invention for inducing an antigen-specific immune response can be used to treat individuals having a variety of pathological conditions. For example, cancer vaccines have been used effectively for treating melanoma and breast cancers. Vaccines have been used for treatment of inflammatory diseases such as asthma (Scanga C. B and Le Gros, G., Drugs 59(6), 1217-1221 (2000)), infectious diseases of pathogenic bacteria such as H. pylori, pathogenic viruses such as human papilloma virus and HIV (Sutton P. and Lee, A, Aliment Pharmacol. 14: 1107-1118 (2000)), protozoa, autoimmune diseases such as diabetes (von Herrath and Whitton, Ann. Med. 32: 285-292 (2000)) and degenerative diseases such as Alzheimer's disease (Youngkin, S. G., Nat. Med., 7(1): 18-19 (2001)). Therefore, a vaccine used in the methods of the invention for inducing an antigen-specific immune response can be administered to an individual for treatment of a variety of pathological conditions, including proliferative disease, infectious disease, inflammatory disease and degenerative disease.

A variety of antigens can be used in combination with an immunomodulatory flagellin peptide of the invention for preparing a vaccine. Microorganisms such as viruses, bacteria and parasites contain substances that are not normally present in the body. These substances can be used as antigens to produce an immune response to destroy both the antigen and cells containing the antigen, such as a bacterial cell or cancer cell.

For example, isolated or crude antigens of microbial pathogens can be used in vaccines to treat infectious disease; isolated or crude tumor cell antigens can be used in vaccines to treat cancer; isolated or crude antigens known to be associated with a pathologically aberrant cell can be used to treat a variety of diseases in which it is beneficial to target particular cells for destruction.

A variety of substances can be used as antigens in a vaccine compound or formulation. For example, attenuated and inactivated viral and bacterial pathogens, purified macromolecules, polysaccharides, toxoids, recombinant antigens, organisms containing a foreign gene from a pathogen, synthetic peptides, polynucleic acids, antibodies and tumor cells can be used to prepare a vaccine useful for treating a pathological condition. Therefore, an immunomodulatory flagellin peptide of the invention can be combined with a wide variety of antigens to produce a vaccine useful for inducing an immune response in an individual. Those skilled in the art will be able to select an antigen appropriate for treating a particular pathological condition and will know how to determine whether a crude or isolated antigen is favored in a particular vaccine formulation.

An isolated antigen can be prepared using a variety of methods well known in the art. A gene encoding any immunogenic polypeptide can be isolated and cloned, for example, in bacterial, yeast, insect, reptile or mammalian cells using recombinant methods well known in the art and described, for example in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1992) and in Ansubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1998). A number of genes encoding surface antigens from viral, bacterial and protozoan pathogens have been successfully cloned, expressed and used as antigens for vaccine development. For example, the major surface antigen of hepatitis B virus, HbsAg, the b subunit of choleratoxin, the enterotoxin of E. coli, the circumsporozoite protein of the malaria parasite, and a glycoprotein membrane antigen from Epstein-Barr virus, as well as tumor cell antigens, have been expressed in various well known vector/host systems, purified and used in vaccines. An immunomodulatory flagellin peptide, polypeptide or modification thereof induces an innate immune response through TLR5 that can beneficially enhance an immune response to a recombinant antigen.

A pathologically aberrant cell to be used in a vaccine can be obtained from any source such as one or more individuals having a pathological condition or ex vivo or in vitro cultured cells obtained from one or more such individuals, including a specific individual to be treated with the resulting vaccine.

Those skilled in the art will be able to determine if a vaccine compound or formulation induces an innate, humoral, cell-mediated, or any combination of these types of immune response, as methods for characterizing these immune responses are well known in the art. For example, the ability of a vaccine compound or formulation to induce an innate immune response through TLR5 can be determined using methods described herein as well as other methods. Such methods for detecting an innate immune response can be generally performed within hours of vaccine administration. The ability of a vaccine compound or formulation to induce a humoral response can be determined by measuring the titer of antigen-specific antibodies in an animal primed with the vaccine and boosted with the antigen, or determining the presence of antibodies cross-reactive with an antigen by ELISA, Western blotting or other well-known methods. Cell-mediated immune responses can be determined, for example, by measuring cytotoxic T cell response to antigen using a variety of methods well known in the art. Methods of detecting humoral and cell-medicated immune responses can be generally performed days or weeks after vaccine administration.

A combination of an antigen or immunomodulatory molecule and an immunomodulatory flagellin peptide, polypeptide or modification thereof, can be tested in a variety of preclinical toxicological and safety studies well known in the art. For example, such a combination can be evaluated in an animal model in which the antigen has been found to be immunogenic and that can be reproducibly immunized by the same route proposed for human clinical testing. A combination of an antigen or immunomodulatory molecule and an immunomodulatory flagellin peptide or modification thereof can be tested, for example, by an approach set forth by the Center for Biologics Evaluation and Research/Food and Drug Administration and National Institute of Allergy and Infectious Diseases (Goldenthal, K L et al. AID Res Hum Retroviruses, 9: S45-9 (1993)).

Those skilled in the art will know how to determine for a particular combination of antigen or immunomodulatory molecule and immunomodulatory flagellin polypeptide modification thereof, the appropriate antigen payload, route of immunization, volume of dose, purity of antigen, and vaccination regimen useful to treat a particular pathological condition in a particular animal species.

The invention provides a method of inducing a TLR5-mediated response. The method involves administering to a TLR5-contain cell an effective amount of an immunomodulatory flagellin peptide having at least about 10 amino acids of substantially the amino acid sequence of SEQ ID NO:2, or a modification thereof.

A TLR5-mediated response can be assessed in a cell or animal because TLR5 stimulates cellular activities that stimulate the immune response that occurs in an animal. For example, flagellin binding to TLR5 induces cellular events such as an increase in the amount or activity of cytokines, such as TNFa, IL-1 and IL-6. These cytokines in turn regulate the activities of immune system cells. Therefore a TLR5-mediated response can be determined by examining an immune responses in an animal and by observing particular immune system cell activities. Determination of immune responses in an animal is discussed below. Determination of immune system cell activities can be performed, for example, by observing or measuring the amount of activity of immunomodulatory molecules produced by specific types of immune cells. Cytokine production by macrophages is an exemplary immune cell activity that can be conveniently measured using methods well known in the art and those described herein. A biological activity of a cytokine can also be assessed using methods well known in the art. TNFa activities include, for example, inducing the production of IL-1 and IL-6, activation of neutrophils and endothelial cells in inflammation, inducing acute phase reactants in liver, inducing fever. IL-1 activities include, for example, activating of endothelial cells in inflammation and coagulation, inducing acute phage reactants in liver, inducing fever and stimulating T cell proliferation. IL-6 activities include, for example, stimulating proliferation of mature B cells and inducing their final maturation into antibody-producing plasma cells, inducing IL-2 receptor expression, inducing acute phase reactants in liver, and co-stimulation of thymocytes in vitro. A regulatory effect of IL-6 is inhibition of TNFa production, providing negative feedback for limiting the acute inflammatory response (Feghali, C. A. and Wright, T. M., Frontiers in Bioscience, 2, d12-26 (1997) provides a summary of cytokine activities).

The invention provides a method of inducing an immune response in an individual having a pathological condition. The method involves administering to said individual an immunogenic amount of an immunomodulatory flagellin peptide having at least about 10 amino acids of substantially the amino acid sequence of SEQ ID NO:2, or a modification thereof.

As described above, an immunomodulatory flagellin peptide can be used to beneficially boost a general immune response in an individual having a pathological condition by stimulating an innate immune response. An increased immune response can ameliorate a pathological condition as well as prevent a pathological condition in a healthy individual, or individual not having a pathological condition. Therefore, an immunomodulatory flagellin peptide can be administered prophylactically to an individual not having a pathological condition, if desired.

The invention provides another method of modulating an immune response in an individual having a pathological condition. The method involves administering to the individual a combination of an immunogenic amount of an immunomodulatory flagellin peptide having at least about 10 amino acids of substantially the amino acid sequence of SEQ ID NO:2, or a modification thereof, and another immunomodulatory molecule.

As described above, a combination of an immunomodulatory flagellin peptide with another immunomodulatory molecule can be used to advantageously induce or modulate an immune response. An immune response can be induced by combining an immunomodulatory flagellin peptide with another immunomodulatory molecule that induces an immune response in a general manner, such as an adjuvant, or can be combined with an immunomodulatory molecule that induces a particular alteration in an immune cell activity. Such immunomodulatory molecules are described herein.

Modulating an immune response is useful for promoting a more effective or more normal immune response in an individual having a pathological condition. As described above, alterations in normal cytokine levels are associated with various pathological conditions. An immunomodulatory flagellin peptide or combination with another immunomodulatory molecule can be used to modulate cytokine levels in an individual by inducing the production of immunomodulatory molecules, such as cytokines including TNFα, IL-1, and IL-6 through TLR5, and inducing the production of suppression of the same or different immunomodulatory molecules through the activity of the administered immunomodulatory molecule. Therefore, the immunomodulatory flagellin peptides of the invention can be combined with immunomodulatory molecules that alter an immune response by stimulating or inhibiting the cellular functions of immune system cells.

A variety of immunomodulatory molecules can be used in combination with an immunomodulatory flagellin peptide or modification thereof of the invention to alter an immune response in an individual. The type of alteration desired will determine the type of immunomodulatory molecule selected to be combined with an immunomodulatory flagellin peptide. For example, to promote an innate immune response, a immunomodulatory flagellin peptide can be combined with another immunomodulatory molecule that promotes an innate immune response, such as a PAMP or conserved region known or suspected of inducing an innate immune response. A variety of PAMPs are known to stimulate the activities of different members of the toll-like family of receptors. Such PAMPs can be combined to stimulate a particular combination of toll-like receptors that induce a beneficial cytokine profile. For example, PAMPs can be combined to stimulate a cytokine profile that induces a TH1 or TH2 immune response.

Other types of immunomodulatory molecules that promote humoral or cell-mediated immune responses can be combined with a flagellin molecule of the invention. For example, cytokines can be administered to alter the balance of TH1 and TH2 immune responses. Those skilled in the art will know how to determine the appropriate cytokines useful for obtaining a beneficial alteration in immune response for a particular pathological condition.

Immunomodulatory molecules that target antigens and cells displaying antigens for destruction can be combined with a flagellin molecule of the invention. For example, the effectiveness of monoclonal antibodies and ADCC targeting molecules that recognize a particular antigen on an unwanted cell, such as a pathologically aberrant cell can be increased when administered with a flagellin molecule of the invention. Immunomodulatory molecules that stimulate or suppress cellular activities such as proliferation, migration, activation, interaction and differentiation can be combined with a flagellin molecule of the invention. For example, IL-2 can be used to stimulate proliferation of immune system cells, certain interferons can be used to interfere with the rapid growth of cancer cells or to interfere with angiogenesis, and ganulocyte-colony stimulating factor can be used to increase production of certain types of immune system cells and blood cells. A variety of immunostimulating and immunosupressing molecules and modalities are well known in the art and can be used in combination with a flagellin polypeptide, peptide or modification thereof, of the invention. A flagellin molecule of the invention increases the beneficial effect of an immunomodulatory molecule by inducing TLR5-mediated production of immunomodulatory molecules that function in concert with a selected immunomodulatory molecule to produce a desired cytokine profile or cellular activity, or prime the adaptive immune response to respond to the selected immunomodulatory molecule.

The methods of the invention for using immunomodulatory flagellin peptides to induce an immune response are also applicable to a flagellin polypeptide, or a modification thereof. Accordingly, the invention provides a method of inducing an immune response in an individual, including a human, having a pathological condition. The method involves administering to the individual an immunogenic amount of an immunomodulatory flagellin polypeptide, or modification thereof, when the flagellin polypeptide induces an immune response.

An immunomodulatory flagellin peptide of the invention binds to TLR5, and stimulates a TLR5 activity. The ability of an immunomodulatory flagellin peptide or modification thereof to bind to TLR5 or stimulate a TLR5 activity can be determined using methods known in the art. Methods of determining specific binding interactions of flagellin peptides and modifications thereof with TLR5 can be determined using well known methods in the art such as methods of trapping ligand-receptor complexes using chemical cross-linking, and competitive inhibition of reagents specific for TLR5 such as specific flagellin peptides or modifications, antibodies or other TLR-5 specific reagents.

Methods of determining TLR5 functional activities in response to an immunomodulatory flagellin peptide or modification thereof include methods described herein, in Examples I through IV, as well as methods known in the art. A variety of methods well known in the art can be used for determining transcription factor activities. For example, fos, jun, and NF-kB activation in response to TLR5 binding to a flagellin molecule can be detected by electrophoretic mobility shift assays well known in the art that detect NF-kB binding to specific polynucleic acid sequences, and promoter-reporter nucleic acid constructs such that, for example, b-lactamase, luciferase, green fluorescent protein or b-galactosidase will be expressed in response to contacting a TLR5 with a flagellin polypeptide, peptide or equivalent thereof. For example, a luciferase reporter plasmid in which luciferase protein expression is driven by one or more NF-kB binding sites can be transfected into a cell, as described in Examples I-IV. Activation of NF-kB results in activation of luciferase reporter expression, resulting in production of luciferase enzyme able to catalyze the generation of a molecule that can be detected by colorimetric, fluorescence, chemilluminescence or radiometric assay.

An amount or activity of a polypeptide, including a cytokine such as TNFa, IL-1 or IL-6, can be a read-out for activation of a TLR5 in response to binding an immunomodulatory flagellin peptide or modification thereof. A variety of methods well known in the art can be used to measure cytokine amounts, such as, for example, flow cytometry methods, immunoassays such as ELISA and RIA, and cytokine RNA protection assays. Commercially available cytokine assay kits, such as ELISA assay formats, can be conveniently used to determine the amount of a variety of cytokines in a sample. Those skilled in the art will determine the particular cytokines to be measured when assessing an immune response in a cell or animal. For example, to determine whether a particular response is characterized as a TH1 or TH2 immune response, those skilled in the art will be able to select appropriate cytokines within the TH1 and TH2 categories, which are well known in the art.

A sample used for determining a TLR5-mediated response or immune response can include, for example, a fluid or tissue obtained from an animal, a cell obtained from an animal fluid or tissue, cultured cells including in vitro and ex vivo cultured cells, and lysates or fractions thereof and cultured cells that express TLR5.

An immune response in an animal is determined by the collective responses of the cells of the immune system. An immune response can be detected by observing various indicators of immune response in an animal. Such indicators include, for example, visible signs of inflammation of tissues, such as swelling, production of antibodies, such as levels of IgA, IgG and IgM in blood and levels of IgA in saliva, alterations in immune cell numbers, such as increased or decreased proliferation of particular immune cells, and in immune cell activities, such as production of immunomodulatory molecules and second messenger molecules. For example, an immune response to a particular antigen can be observed in a animal using methods well known in the art such as delayed hypersensitivity skin tests. An immune response can be determined by the presence of antibodies cross reactive with an antigen, such as by ELISA and Western blotting, lymphocyte activation tests employing mitogen or antigen stimulation, mixed lymphocyte culture tests, assays for human T and B lymphocytes, flow cytometry and cell sorting to characterize populations of immune system cells obtained from an individual, soluble antigen uptake by macrophages, and tests of neutrophil functions (Stites et al. Basic and Clinical Immunology, 4^(th) edition, Lange Medical Publications, Los Altos, Calif. (1982)). An immune response can also be assessed by examining amounts or activities of immune system mediators, such as cytokines and chemokines, in cells collected from fluids or tissues of animals. A variety of methods are well known in the art for qualitative and quantitative measurement of cytokine amount and bioassay of cytokine activity.

The methods of the invention for inducing an immune response can be used to treat any animal species having an immune response upon treatment with flagellin polypeptide, peptide, or modification thereof, and for which a stimulation of an immune response is desired. Such animals include avian species such as chicken, and mammalian species such as rodent, canine, feline, bovine, porcine and human subjects. Methods for using adjuvants with vaccines and vaccinating animals are well known in the art and are routinely used in laboratory animals. Those skilled in the art will be able to determine if a particular animal species has a flagellin-stimulated TLR5-mediated innate immune response.

A vaccine to be used in the methods of the invention for inducing an immune response can be administered as a solution or suspension together with a pharmaceutically acceptable medium. Such a pharmaceutically acceptable medium can be, for example, water, phosphate buffered saline, normal saline or other physiologically buffered saline, or other solvent or vehicle such as glycol, glycerol, and oil such as olive oil or an injectable organic ester. A pharmaceutically acceptable medium can also contain liposomes or micelles, and can contain immunostimulating complexes prepared by mixing polypeptide or peptide antigens with detergent and a glycoside, such as Quil A. Further methods for preparing and administering an immunomodulatory flagellin polypeptide or peptide, or modification in a pharmaceutically acceptable medium are presented below, in reference to compounds that induce a TLR-mediated response.

The immunomodulatory flagellin polypeptides, peptides and modifications thereof used in the methods of the invention can be administered by a variety of routes to stimulate an immune response. For example, these immunomodulatory molecules can be delivered intranasally, subcutaneously, intradermally, intralymphatically, intra-muscularly, intratumorally, orally, intravesically, intraperitoneally and intracerebrally. Oral administration is convenient and relatively safe. Oral vaccination protocols can be useful for inducing the state of immunological tolerance which normally occurs in response to most soluble antigens and the proteolytic degradation of antigen preparations in the digestive tract. Nasal delivery routes may be useful for inducing both mucosal and systemic immune responses. A variety of devices are under development for convenient and effective delivery of formulations to the nasal cavity and pulmonary tissues. Those skilled in the art will know how to select appropriate delivery routes for particular formulations of flagellin polypeptides, peptides and modifications thereof.

The invention provides a screening composition consisting of an immunomodulatory flagellin peptide comprising at least about 10 amino acids of substantially the amino acid sequence GAVQNRFNSAIT (SEQ ID NO:2), or a modification thereof, and having toll-like receptor 5 (TLR5) binding, and a TLR5. The composition is useful for identifying agonists, antagonists and ligands for TLR5. The characteristics of an immunomodulatory flagellin peptide comprising at least about 10 amino acids of substantially the amino acid sequence GAVQNRFNSAIT (SEQ ID NO:2), or a modification thereof, and having toll-like receptor 5 (TLR5) binding, and preparation of a flagellin peptide are described herein. Similarly, the characteristics of a TLR5 polypeptide and modifications thereof that have a TLR5 activity, and methods for preparing a TLR5 polypeptide to be used in the methods of the invention are described herein. Chimeric TLR5s, such as the CD4-TLR5 described herein in Example I, are included in the screening compositions of the invention.

The screening composition of the invention includes, for example, cells, cell extracts and artificial signaling systems that contain a TLR5 polypeptide or modification thereof. The cell compositions of the invention include any cell in which TLR5 can couple to a signal transduction pathway to produce a detectable signal in response to an agonist, such as flagellin or a flagellin peptide. Such cells include insect cells such as Drosophila cells, yeast cells such as S. cerevisiae, prokaryotic cells such as E. coli, amphibian cells such as Xenopus oocytes, and vertebrate cells such as mammalian primary cells, such as macrophages. Primary cells such as macrophages and other lymphocytes can be conveniently isolated from blood using methods well known in the art. Cells obtained from transgenic animals, such as transgenic mice that have been engineered by known methods of express recombinant TLR5 or TLR5 signal transduction components are also included in the screening compositions of the invention. Cell lines prepared from any of theses cell types, such as S2, CHO, NIH-3T3, 293 and HeLa cells are also included in a screening composition of the invention.

The screening compositions of the invention can include crude or partially purified lysates or extracts of the cell compositions of the invention, and reconstituted signaling systems. Artificial signaling systems include, for example, natural or artificial lipid bilayers, such as a liposome or micelle, which promote an active conformation of a TLR5. The compositions can further contain cellular fractions or isolated components necessary for producing and detecting the desired predetermined signal.

The invention provides a method of screening for a TLR5 ligand, agonist or antagonist. The method involves, (a) contacting a TLR5 with a candidate compound in the presence of a flagellin polypeptide or immunomodulatory flagellin peptide under conditions wherein binding of the flagellin polypeptide or immunomodulatory flagellin peptide to the TLR5 produces a predetermined signal; (b) determining the production of the predetermined signal in the presence of the candidate compound; and (c) comparing the predetermined signal in the presence of the candidate compound with a predetermined signal in the absence of the candidate compound, wherein a difference between the predetermined signals in the presence and absence of the candidate compound indicates that the compound is a TLR5 ligand, agonist or antagonist.

TLR5 can produce a variety of predetermined signals useful in the methods of the invention for identifying a TLR5 ligand, agonist or antagonist. TLR5 has an extracellular domain that participates in ligand recognition and intracellular domain that contain a conserved region called the Toll/IL-IR homology (TIR) domain that, upon activation, recruits an adaptor protein, MyD88. Through an amino terminal death domain, MyD88 recruits the serine kinase IRAK to propagate a pro-inflammatory signal through binding to TRAF6, which then binds to other molecules that participate in the TLR5 signaling cascade. Immunomodulatory flagellin peptides and modifications binding to TLR5 induces signal transduction events which result in, for example, stimulating NF-kB activity and inducing production of gene products of NF-kB-regulated genes, such as TNFa, IL-1 and IL-6, as well as stimulating AP-1 transcription factors fos and jun. Therefore, a predetermined signal can include a signal produced by an immunomodulatory flagellin polypeptide or peptide or modification binding to TLR5, a signal produced by a TLR5 intracellular signal transduction even, such as kinase or phosphatase activity or protein-protein interactions, by activation of fos, jun or NF-kB, and by an amount or activity of a fos-, jun- or NF-kB-regulated gene or gene product, such as TNFa, IL-1 and IL-6.

A variety of low- and high-throughput assays suitable for detecting selective binding interactions between a receptor and a ligand are known in the art. Both direct and competitive assays can be performed, including, for example, fluorescence correlation spectroscopy (FCS) and scintillation proximity assays (SAP) reviewed in Major, J. Receptor and Signal Transduction Res. 15: 595-607 (1995); and in Sterrer et al., J. Receptor and Signal Transduction Res. 17: 511-520 (1997)). Other assays for detecting binding interactions include, for example, ELISA assays, FACS analysis, and affinity separation methods. Such assays can involve labeling a TLR5 ligand, such as flagellin or a flagellin peptide, with a detectable moiety such as a radiolabel, fluorochrome, ferromagnetic substance, or luminescent substance. A detectably labeled flagellin polypeptide or peptide can be prepared using methods well known in the art. Receptor binding assays, including high-throughput automated binding assays, and methods of determining binding affinity from such assays, are well known in the art, and any suitable direct or competitive binding assay can be used. Exemplary high-throughput receptor binding assays are described, for example, in Mellentin-Micelotti et al., Anal. Biochem. 272: P182-190 (1999); Zuck et al., Proc. Natl. Acad. Sci. USA 96: 11122-11127 (1999); and Zhang et al., Anal. Biochem. 268; 134-142 (1999).

A variety of methods well known in the art can be used to detect activation of transcription factors, such as NF-kB, in low- or high-throughput formats. The methods described herein and in the Examples can be adapted to formats suitable for candidate compound screening.

A variety of low- and high-throughput assays suitable for detecting amounts and activities of polypeptides such as cytokines are known in the art. Methods for detecting polypeptides, include, for example, flow cytometric measurements as described herein, immunodetection methods such as radioimmune assay (RIA), ELISA, immunoprecipitation and Western blotting. Assay of the activity of a cytokine include function bioassays and detection of amounts of polypeptides regulated by a particular cytokine. Those skilled in the art can determine an appropriate method for detecting an activity of a particular cytokine.

Suitable conditions under which TLR5 produces a predetermined signal in response to a flagellin polypeptide, peptide or modification can be determined by those skilled in the art, and will depend on the particular predetermined signal selected. Exemplary conditions for determining the production of a predetermined signal are provided herein in Examples I-IV. Any known or predicted TLR5-mediated cellular event, such as elicitation of second messengers, induction of gene expression or altered cellular proliferation, differentiation or viability can be a predetermined signal that is an indication of activation of signal transduction through TLR5.

Assays for detecting a predetermined signal produced by binding of flagellin or flagellin peptide to TLR5 can be performed, for example, with whole cells that express TLR5, membrane fractions, or artificial systems, as described herein, or with isolated TLR5 polypeptide, either in solution, in an artificial membrane, or bound to a solid support.

A method of identifying TLR5 agonists and antagonists can be performed either in the presence of a predetermined concentration of a known TLR5 agonist, such as flagellin, flagellin peptide, or modifications thereof, or in the absence of agonist. The agonist can be added either prior to, simultaneously with, or after, addition of the test compound. When present, the agonist concentration is preferably within 10-fold of its EC50 under the assay conditions to allow the identification of a compound that competes with a known agonist for signaling through TLR5, or indirectly augments signaling through the receptor. Likewise, a compound that reduces binding between a known agonist and its receptor, or indirectly decreases signaling through the receptor, can also be identified.

The method of screening to identify a ligand, agonist or antagonist of TLR5 involve testing a candidate compound. A candidate compound can be any substance, molecule, compound, mixture of molecules or compounds, or any other composition. The candidate compounds can be small molecules or macromolecules, such as biological polymers, including proteins, polysaccharides and nucleic acids. Sources of candidate compounds which can be screened for a ligand, agonist or antagonist of TLR5 include, for example, libraries of small molecules, peptides and polypeptides.

Additionally, candidate compounds can be preselected based on a variety of criteria. For example, suitable candidate compounds can be selected as having known ligand, agonist or antagonist activity. Alternatively, candidate compounds can be selected randomly. Candidate compounds can be administered to the reaction system at a single concentration or, alternatively, at a range of concentrations to determine, for example, an EC50 or IC50 of a candidate compound.

The method of screening for TLR5 ligands, agonists or antagonists can involve groups or libraries of compounds. Methods for preparing large libraries of compounds, including simple or complex organic molecules, carbohydrates, peptides, peptidomimetics, polypeptides, nucleic acids, antibodies, and the like, are well known in the art. Libraries containing large numbers of natural and synthetic compounds can be obtained from commercial sources.

The number of different candidate compounds to examine using the methods of the invention will depend on the application of the method. It is generally understood that the larger the number of candidate compounds, the greater the likelihood of identifying a compound having the desired activity in a screening assay. Large numbers of compounds can be processed in a high-throughput automated format.

The TLR5 agonists, antagonists and ligands identified using the methods and compositions described herein, are potential therapeutic compounds that can be administered to an individual, such as a human or other mammal, in an effective amount to increase or decrease signaling through TLR5, for example, to alter an immune response or treat a TLR5-associated condition. Such compounds can be used analogously to immunomodulatory compounds useful for augmenting and altering an immune response, as described above. For example, a compound can be used to induce a general immune response and to induce a specific immune response in the presence of an antigen and to alter the level of a particular cytokine in an individual having a pathological condition.

The TLR5 agonists and antagonists, immunomodulatory flagellin peptides, polypeptides and modifications thereof, are useful for ameliorating, or reducing the severity of a pathological condition. Reduction in severity includes, for example, an arrest or decrease in clinical symptoms, physiological indicators, biochemical markers or metabolic indicators of disease. Those skilled in the art will know, or will be able to determine the appropriate clinical symptoms, physiological indicators, biochemical markers or metabolic indicators to observe for a particular pathological condition. To prevent a disease means to preclude the occurrence of a disease or restoring a diseased individual to their state of health prior to disease.

In addition to applications described herein for agonists and antagonists, a TLR5 ligand can be used, for example, to specifically target a diagnostic moiety to cells and tissues that express TLR5, such as monocytes, immature dendritic cells, epithelial cells, and other cells involved in an immune response. Thus, a TLR5 ligand can be labeled with a detectable moiety, such as a radiolabel, fluorochrome, ferromagnetic substance, or luminescent substance, and used to detect normal or abnormal expression of TLR5 polypeptide in an isolated sample or in vivo diagnostic imaging procedures.

A heterologous amino acid sequence can be advantageously used to provide a tag for detection or purification or to impart an activity to a reference polypeptide or peptide, such as an enzyme activity, a biological activity, an immunological activity or stability. An immunomodulatory flagellin peptide, polypeptide or modification thereof, or TLR5 polypeptide can contain a heterologous amino acid sequence, or amino acid sequence not present in the native amino acid sequence of a reference polypeptide or peptide and not represented by a modification of a reference polypeptide or peptide. A heterologous amino acid sequence can be of any size in relation to the reference amino acid sequence. A TLR5 polypeptide containing the heterologous sequence of CD4 is a specific example of such a modification and is described further in Example I. The described CD4-TLR5 chimera is identified by the amino acid sequence of SEQ ID NO:10, encoded by the nucleic acid sequence of SEQ ID NO:9. A chimeric TLR5 can be prepared using cloning methods well known in the art. For example, a chimeric polypeptide can be produced by amplifying by PCR a nucleotide sequence encoding a portion of a selected polypeptide using sequence specific primers. Primers useful for amplifying a TLR5 include, for example, huTLR5-A6: TTAAAGTGGTACCAGTTCTCCCTTTTCATTGTATGCACT (SEQ ID NO:35) and huTLR5DNS: CGGGATCCCGTTAGGAGATGGTTGCTACAGTTTGC (SEQ ID NO:36). A portion of a TLR5 nucleotide sequence, such as a sequence amplified using such primers can be fused to a nucleotide sequence encoding a heterologous amino acid sequence. A variety of methods for generating nucleic acid sequences encoding chimeric polypeptides are well known to those skilled in the art.

The polypeptides and peptides described herein, including immunomodulatory flagellin peptides, flagellin polypeptide, TLR5 polypeptides and fragments thereof can be prepared using a variety of protein expression systems well known in the art, including prokaryotic and eukaryotic expression systems. Prokaryotic expression systems are advantageous due to their ease in manipulation, low complexity growth media, low cost of growth media, rapid growth rates and relatively high yields. Well known prokaryotic expression systems include, for example, E. coli bacterial expression systems based on bacteriophage T7 RNA polymerase, the trc promoter, the araB promoter and bacillus expression. Eukaryotic expression systems are advantageous because expressed polypeptides can contain eukaryotic post-translational modifications such as O-linked glycosylation, phosphorylation and acetylation and can have improved protein folding. Well known eukaryotic expression systems include, for example, expression in yeast, such as Pichia pastoris and Pichia methanolica, expression in insect systems such as the Drosophila S2 system and baculovirus expression systems and expression in mammalian cells using adenoviral vectors and cytomegalovirus promoter-containing vectors.

An immunomodulatory flagellin peptide, polypeptide, TLR5 or fragments thereof can be purified using a variety of methods of protein purification well known in the art. Biochemical purification can include, for example, steps such as solubilization of the polypeptide or peptide-expressing cell, isolation of the desired subcellular fractions, chromatography, such as ion exchange, size, or affinity-based chromatographies, electrophoresis, and immunoaffinity procedures. Other well-known methods are described in Deutscher et al., Guide to Protein Purification: Methods in Enzymology Vol. 182, (Academic Press, (1990)). An exemplary method for purifying a flagellin peptide is provided in Example III. The methods and conditions for biochemical purification of a polypeptide of the invention can be chosen by those skilled in the art, and the purification monitored, for example, by staining SDS-PAGE gels containing protein samples, by immunodetection methods such as Western blotting and ELISA, and by functional assay of immunogenic activity of flagellin or a TLR5 activity of TLR5.

An immunomodulatory flagellin peptide, polypeptide, TLR5 or fragments thereof can be modified, for example, to increase polypeptide stability, alter an activity, facilitate detection or purification, or render the enzyme better suited for a particular application, such as by altering substrate specificity. Computer programs known in the art can be used to determine which amino acid residues of a immunomodulatory flagellin peptide, flagellin polypeptide or TLR5 can be modified as described above without abolishing a corresponding activity (see, for example, Eroshkin et al., Comput. Appl. Biosci. 9: 491-497 (1993)). In addition, structural and sequence information can be used to determine the amino acid residues important for activity. For example, a comparisons of flagellin amino acid sequences, such as that shown in FIG. 7 can provide guidance in determining amino acid residues that can be altered without abolishing flagellin or flagellin peptide activity by indicating amino acid residues that are conserved across species. Conserved regions of flagellin are well known in the art and have been described, for example, in Mimori-Kiyosue, et al., J. Mol. Viol. 270: 222-237, (1997). A crystal structure of flagellin can also provide guidance for making flagellin modifications (Samatey et al. Nature, 410: 331-337 (2001)). Similarly, amino acid sequence comparisons between the disclosed murine TLR5, TLR5s of other species, and other toll-like receptor family members can provide guidance for determining amino acid residues important for activity.

An isolated TLR5 is a TLR5 removed from one or more components with which it is naturally associated. Therefore, an isolated TLR5 can be a cell lysate, cell fraction, such as a membrane fraction, or a purified TLR5 polypeptide. An isolated TLR5 can include a liposome or other compound or matrix that stabilizes or promotes an active conformation of the receptor.

For treating or reducing the severity of a pathological condition a TLR5 agonist or antagonist, immunomodulatory flagellin peptide, polypeptide or modification thereof, including a vaccine, can be formulated and administered in a manner and in an amount appropriate for the condition to be treated; the weight, gender, age and health of the individual; the biochemical nature, bioactivity, bioavailability and side effects of the particular compound; and in a manner compatible with concurrent treatment regimens. An appropriate amount and formulation for a particular therapeutic application in humans can be extrapolated based on the activity of the compound in recognized animal models of the particular disorder.

Animal models of aberrantly proliferative diseases can be used to assess a formulation of compound, including a vaccine or adjuvant containing an immunomodulatory flagellin peptide, polypeptide or modification thereof, for an amount sufficient to induce an immune response or ameliorate disease symptoms. Animal models of such pathological conditions well known in the art which are reliable predictors of treatments in human individuals for include, for example, animal models for tumor growth and metastasis, infectious diseases and autoimmune disease.

There are numerous animal tumor models predictive of therapeutic treatment which are well known in the art. These models generally include the inoculation or implantation of a laboratory animal with heterologous tumor cells followed by simultaneous or subsequent administration of a therapeutic treatment. The efficacy of the treatment is determined by measuring the extent of tumor growth or metastasis. Measurement of clinical or physiological indicators can alternatively or additionally be assessed as an indicator of treatment efficacy. Exemplary animal tumor models can be found described in, for example, Brugge et al., Origins of Human Cancer, Cold Spring Harbor Laboratory Press, Plain View, N.Y., (1991).

Similarly, animal models predictive for infectious disease also follow a similar approach. Briefly, laboratory animals are inoculated with an infectious agent and the progression of the infection is monitored by, for example, clinical symptoms, growth culture of the agent from an infected tissue sample or biopsy in the presence or absence of the therapeutic treatment. The reduction in severity of the diagnostic indicator is indicative of the efficacy of the treatment. A variety of animal models for infectious diseases are well known to those skilled in the art.

One animal model predictive for autoimmune diseases is Experimental allergic encephalomyelitis (EAE), also called experimental autoimmune encephalomyelitis. Although originally characterized as a model for neurological autoimmune disease such as human multiple sclerosis, the use of this model to predict treatments of other autoimmune diseases has been widely accepted. EAE is induced in susceptible animals by active immunization with myelin basic protein (MPB) or by passive transfer of MBP-specific T helper lymphocytes. Progression of the disease is characterized by chronic relapsing paralysis and central nervous system demyelination, which can be monitored by observation or by immunological determinants such as delayed-type hypersensitivity (DTH; a measure of cell mediated immunity) response to the immunogen. Efficacy of a therapeutic treatment is compared to progression of the disease in the absence of treatment. A reduction in severity of EAE symptoms or immunological determinants in treated animals is indicative of the efficacy of the therapeutic treatment. For a review of autoimmune disease models see, for example, Urban et al., Cell, 54: 577-592 (1988); Brostoff et al., Immunol. Ser. 59: 203-218 (1993) and U.S. Pat. Nos. 5,614,192 and 5,612,035.

A growing number of human diseases have been classified as autoimmune and include, for example, rheumatoid arthritis, myasthenia gravis, multiple sclerosis, psoriasis, systemic lupus erythmatosis, autoimmune thyroiditis, Graves' disease, inflammatory bowel disease, autoimmune uveoretinitis, polymyositis and diabetes. Animal models for many of these have been developed and can be employed analogously as the EAE model described above predictive assessment of therapeutic treatments using the compounds, vaccines and adjuvants in the methods of the invention. Other reliable and predictive animal models are well known in the art and similarly can be used to assess a compound formulation, including vaccine and adjuvant formulations containing an immunomodulatory flagellin peptide, polypeptide or modification thereof.

The total amount of a compound including an immunomodulatory flagellin peptide, polypeptide or modification thereof, that modulates a TLR5-mediated immune response can be administered as a single dose or by infusion over a relatively short period of time, or can be administered in multiple doses administered over a more prolonged period of time. Additionally, a compound can be administered in a slow-release matrix, which can be implanted for systemic delivery at or near the site of the target tissue.

A compound that modulates a TLR5-mediated immune response can be administered to an individual using a variety of methods known in the art including, for example, intravenously, intramuscularly, subcutaneously, intraorbitally, intracapsularly, intraperitoneally, intracistemally, intra-articularly, intracerebrally, orally, intravaginally, rectally, topically, intranasally, or transdermally.

A compound that modulates a TLR5-mediated immune response can be administered to a subject as a pharmaceutical composition comprising the compound and a pharmaceutically acceptable carrier. The choice of pharmaceutically acceptable carrier depends on the route of administration of the compound and on its particular physical and chemical characteristics. Pharmaceutically acceptable carriers are well known in the art and include sterile aqueous solvents such as physiologically buffered saline, and other solvents or vehicles such as glycols, glycerol, oils such as olive oil and injectable organic esters. A pharmaceutically acceptable carrier can further contain physiologically acceptable compounds that stabilize the compound, increase its solubility, or increase its absorption. Such physiologically acceptable compounds include carbohydrates such as glucose, sucrose or dextrans; antioxidants, such as ascorbic acid or glutathione; chelating agents; and low molecular weight proteins. As described above in reference to vaccines, such routes of administration are also applicable to administration of an immunomodulatory flagellin peptide, polypeptide or modification thereof.

In addition, a formulation of a compound that modulates a TLR5-mediated immune response can be incorporated into biodegradable polymers allowing for sustained release of the compound, the polymers being implanted in the vicinity of where drug delivery is desired, for example, at the site of a tumor or implanted so that the compound is released systemically over time. Osmotic minipumps also can be used to provide controlled delivery of specific concentrations of a compound through cannulae to the site of interest, such as directly into a tumor growth or other site of a pathology involving a perturbation state. The biodegradable polymers and their use are described, for example, in detail in Brem et al., J. Neurosurg. 74: 441-446 (1991). These methods, in addition to those described above in reference to vaccines, are applicable to administering an immunomodulatory flagellin peptide, polypeptide or modification thereof to induce an immune response.

The methods of treating a pathological condition additionally can be practiced in conjunction with other therapies. For example, for treating cancer, the methods of the invention can be practiced prior to, during, or subsequent to conventional cancer treatments such as surgery, chemotherapy, including administration of cytokines and growth factors, radiation or other methods known in the art. Similarly, for treating pathological conditions which include infectious disease, the methods of the invention can be practiced prior to, during, or subsequent to conventional treatments, such as antibiotic administration, against infectious agents or other methods known in the art. Treatment of pathological conditions of autoimmune disorders also can be accomplished by combining the methods of the invention for inducing an immune response with conventional treatments for the particular autoimmune diseases. Conventional treatments include, for example, chemotherapy, steroid therapy, insulin and other growth factor and cytokine therapy, passive immunity and inhibitors of T cell receptor binding. The methods of the invention can be administered in conjunction with these or other methods known in the art and at various times prior, during or subsequent to initiation of conventional treatments. For a description of treatments for pathological conditions characterized by aberrant cell growth see, for example, The Merck Manual, Sixteenth Ed, (Berkow, R., Editor) Rahway, N. J., 1992.

As described above, administration of a compound, immunomodulatory flagellin peptide, flagellin polypeptide or modification thereof can be, for example, simultaneous with or delivered in alternative administrations with the conventional therapy, including multiple administrations. Simultaneous administration can be, for example, together in the same formulation or in different formulations delivered at about the same time or immediately in sequence. Alternating administrations can be, for example, delivering an immunomodulatory flagellin peptide or polypeptide formulation and a conventional therapeutic treatment in temporally separate administrations. As described previously, the temporally separate administrations of a compound, immunomodulatory flagellin peptide, polypeptide or modification thereof, and conventional therapy can similarly use different modes of delivery and routes.

The invention provides a method of using a signal produced in response to flagellin binding to TLR5 to detect bacterial contamination in a sample. The method can be used to detect picogram amounts of flagellin in a sample.

Food-born diseases resulting from the presence of harmful bacteria account for 325,000 hospitalizations and 5,000 deaths each year in the United States (National Institutes of Health, Foodborne Diseases NIAID Fact Sheet). The U.S. Centers for Disease Control and Prevention (CDC) estimates that 1.4 million people in the United States are infected each year with Salmonella. Other bacterial pathogens that cause pathological conditions characterized by symptoms ranging from intestinal discomfort to severe dehydration, bloody diarrhea and even death, include enterohemorrhagic E. coli, such as strains designated O157: H7 and O26:H11, Campylobacter strains such as C. jejuni, and Shigella strains such as S. flexneri.

All of these bacterial strains are flagellated, and therefore express flagellin polypeptides. For example, the amino acid sequences of flagellins from Salmonella, E. coli, Campylobacter, Shigella strains are shown in FIG. 7. The methods of the invention for detecting flagellin polypeptides contained in samples suspected of bacterial contamination can be applied to quality assurance protocols for preparation of foods and numerous other applications.

The invention also provides a bioassay for detecting bacterial contamination in a sample. The method involves, (a) contacting the sample with a TLR5 under conditions wherein binding of a flagellin polypeptide or fragment thereof in the sample to the TLR5 produces a predetermined signal, (b) determining the production of the predetermined signal in the presence and absence of the sample, and (c) comparing the predetermined signal in the presence of the sample with a predetermined signal in the absence of the sample, wherein a difference between the predetermined signals in the presence and absence of the sample indicates that the sample contains flagellin.

The methods of the invention for detecting bacterial contamination are based on the finding disclosed herein that flagellin is a ligand for TLR5. Therefore, a flagellin molecule in a sample can bind to a TLR5 and elicit the production of a predetermined signal. A predetermined signal produced by TLR5 in a particular assay system is compared in the presence and absence of a sample known or suspected of containing a bacterial contaminant. A sample known to be free of flagellin can be used as a negative control, while a sample containing a known concentration of flagellin, flagella or bacteria having flagella can be used as a positive control.

A sample to be tested for the presence of flagellin can be any material that is suspected of being contaminated with a gram-positive or gram-negative flagellated bacterium. For example, the method for determining the presence of flagellin can be performed using a sample of a biological fluid, cell, tissue, organ or portion thereof, such as a sample of a tissue to be used for preparing a product, a product for human or animal consumption, such as a food or pharmaceutical preparation, and a product for external application or administration by any route to an animal.

A variety of predetermined signals produced by a TLR5, as discussed above and in the Examples herein, can be used to detect the binding and activation of a TLR5 by a flagellin molecule present in a sample. A variety of methods known in the art, including those described herein can be used to detect a predetermined signal produced by a TLR5.

It is understood that modifications which do not substantially affect the activity of the various embodiments of this invention are also included within the definition of the invention provided herein. Accordingly, the following examples are intended to illustrate but not limit the present invention.

EXAMPLE I Constitutively Active TLR5 Activates NF-kB and TNFa Production

This example shows activation of NF-kB and TNFa production in CHO cells in response to constitutively active TLR5.

To determine if TLR5 activates NF-kB and TNFa production, the activity of a constitutively active form of TLR5 was examined in CHO cells. Constitutively active forms of TLR4 and TLR5 were generated by fusing the extracellular domain of CD4 to the transmembrane and TIR domain of TLR4 or TLR5 (Medzihitov, R. et al. Nature 388, 394-7 (1997); Ozinsky, A. et al., Proc. Natl. Acad. Sci. 97, 13766-13881 (2000)). CD4-TLR5 was constructed by fusing the murine CD4 extracellular domain (amino acids 1-391) to the putative transmembrane and cytoplasmic domains of human TLR5 (amino acids 639-859) and cloning into pEF6-TOPO (pEF6-mCD4-hTLR5). These chimeras, referred to as CD4-TLR4 and CD4-TLR5 were expressed in CHO cells.

For determining NF-kB activity in response to TLR5, CHO cells were transiently transfected with expression vectors for CD4-TLR4, CD4-TLR5, or empty expression vector (control) together with an NF-kB luciferase reporter. NF-kB-induced luciferase activity was measured. CHO cells (CHO-K1) were obtained from ATCC (no. CRL.-9618) and grown in Ham's F-12 medium supplemented with 10% FBS, L-glutamine, penicillin, and streptomycin. CHO cells were transfected by electroporation as described previously (Underhill, D. M. et al., Nature, 401, 811-5 (1999)), with 1 mg of the indicated TLR expression vector, 1 mg of ELAM-firefly luciferase, 0.1 mg of TK-renilla luciferase (Promega). Cells were plated on 96-well plates at 100,000 cells/well, and incubated overnight at 37° C., 5% CO₂. Firefly and renilla luciferase activities were measured using the Dual Luciferase Assay System (Promega, Madison, Wis.). Luciferase activity is expressed as a ratio of NF-kB-dependent ELAM-firefly luciferase activity divided by control thymidine kinase-renilla luciferase activity (relative luciferase units).

For determining TNFα production in response to TLR5, RAW-TTIO Macrophage cells were transfected with a CD4-TLR5 expression vector, and the production of TNFa was measured by flow cytometry, as described previously (Ozinsky, A. et al. Proc. Natl. Acad. Sci. 97, 13766-13771 (2000)). Transfections were performed by electroporation using 10 mg of pEF6-mCD4-hTLR5, and 18 hours later the cells were incubated with 5 mg/ml of brefeldin A for 4 hours to accumulate intracellular pools of newly synthesized TNFa. Cells were fixed, permeabilized, stained for the expression of CD4 (anti-CD4-FITC, Pharmingen) and TNFa (anti-murine TNFa-PE, Pharmingen), and analyzed on a FACscan (Beckton-Dickenson). FACS data were analyzed with WinMDI (Joseph Trotter, Scripps Research Institute, La Jolla, Calif.). Cells were gated to exclude dead cells and for expression of CD4.

FIG. 1 shows that expression of CD4-TLR5 induced NF-kB activation-mediated luciferase production in CHO cells (FIG. 1 a) and TNFa production in mouse macrophages (FIG. 1 b). In FIG. 1 b, the dotted line indicates TNFa produced in cells not expressing CD4-TLR5, and the solid line indicates TNFa produced in cells expressing CD4-TLR5. Thus, homo-oligomerization of the TLR5 signaling domain induces a cellular signal characterized by the induction of NF-kB activity and production of TNFa.

EXAMPLE II Bacterial Culture Supernatants Contain TLR5-Stimulating Activity

This Example shows that bacterial culture supernatants contain TLR5-stimulating activity.

CHO cells expressing human TLR5 and a luciferase-linked reporter were used to screen for PAMPs recognized by the receptor. PAMPS tested included LPS, lipopeptide, yeast, and extracts from E. coli, Pseudomonas, and Listeria. CHO cells were transiently transfected with TLR2, TLR5, or empty expression vectors together with a NF-kB luciferase reporter. The cells were treated with 100 ng/ml LPS, 100 ng/ml lipopeptide, 10⁷ yeast particles/ml, or untreated (control), and luciferase activity was measured. The cells were treated with 67 mg/ml of supernatant from the indicated saturated bacterial cultures, or LB alone (control), and the luciferase activity was measured. Data are representative of 3 independent experiments.

Human TLR5 and TLR2 were generated by PCR from cDNA derived from human peripheral blood mononuclear cells and cloned into pEF6-TOPO (Invitrogen) (pEF6-hTLR5 and pEF6-hTLR2). Murine TLR5 was generated by PCR using cDNA derived from RAW-TT1O cells and cloned into pEF6 (pEF6−mTLR5).

For luciferase assays, CHO cells were transfected by electroporation as described above, with 1 mg of the indicated TLR expression vector, 1 mg of ELAM-firefly luciferase, 0.1 mg of TK-renilla luciferase (Promega, Madison, Wis.). The medium was replaced with medium containing the stimuli at the indicated concentration/dilution. Bacterial lipopeptide and PAM₃CSK₄, were obtained from Roche, LPS (Salmonella minnesota R595) was from List, and yeast particles (zymosan) were from Molecular Probes (Eugene, Oreg.). Cells were stimulated for 5 hours at 37° C., and firefly and renilla luciferase activities were measured using the Dual Luciferase Assay System (Promega).

For preparation of bacterial supernatants, bacteria were grown either in Luria broth (LB) (Escherichia coli TOP 10 (Invitrogen), Salmonella minnesota (ATCC#49284), mutant Salmonella typhimurium (TH4778fliB− fliC+), TH2795 (fliB− fliC−), (Dr. Kelly Hughes, University of Washington), or grown in trypticase soy broth (TSB) (Listeria monocytogenes (10403, gift of Dr. Daniel Portnoy, UCSF), Listeria innocua (ATCC#33090), Bacillus subtilis, and Pseudomonas aeruginosa (Susan R. Swanzy, University of Washington)). Bacteria were grown to saturation (about 16 hours, 37° C. with vigorous aeration). The bacterial culture supernatants were centrifuged for 30 minutes at 2000×g, filtered (0.2 mM), and stored at 4° C. prior to use. For flaA transfections, E. coli TOP10 containing pTrcHis2-flaA or pTrcHis2-flaArev were selected from bacterial plates and grown to OD₆₀₀ of 0.6 in LB with 100 ug/ml ampicillin and 1% w/v glucose. The bacteria were centrifuged for 30 minutes at 2000×g, and split into two LB cultures, one containing 100 mg/ml ampicillin and 1% w/v glucose (to repress flaA) and the other containing 100 mg/ml ampicillin and 1 mM IPTG (to induce flaA). Samples were taken at 4 hours after induction, centrifuged 5 min at 10,000×g, and the supernatants stored at 4° C. before use.

TLR5 did not respond to any of the PAMPs known to stimulate TLR pathways, such as LPS, lipopeptide, yeast cell wall, or peptidoglycan, while CHO cells transfected with TLR2 were stimulated by lipopeptide, yeast cell wall, and peptidoglycan (FIG. 2 a). However, TLR5-stimulating activity was detected in culture supernatants of a variety of Gram-positive and Gram-negative bacteria (FIG. 2 b). The TLR5-stimulating activity of Gram-positive bacteria was not enhanced by co-expression of CD 14. Interestingly, the TOP10 strain of E. coli had very little TLR5 activity (FIG. 2 b), and was used in subsequent reconstitution experiments (see below). Experiments using murine TLR5 yielded similar results.

Thus, the activity of TLR5 was stimulated by a component of bacterial culture supernatants, but not by PAMPs known to stimulate other toll like receptor family members.

EXAMPLE III Purification of TLR5-Stimulating Activity from L. monocytogenes Culture Supernatant

This Example shows the purification of TLR5-simulating activity from L. monocytogenes culture supernatant.

The biological activity recognized by TLR5 was determined to be TCA precipitable, phenol soluble, and sensitive to proteinase K and trypsin digestion. To identify the bacterial components that stimulate TLR5, the supernatant from a saturated L. monocytogenes culture was concentrated, fractionated by reverse-phase chromatography, and each fraction was assessed for TLR5-stimulating activity in CHO cells (FIG. 3 a).

For assessing the TLR-stimulating activity of FPLC fractions, CHO cells were transfected as described in Example I with the addition of 0.1 mg of pNeo/Tak (Underhill et al., Nature 401, 811-5 (1999)), and stable populations of cells expressing the indicated TLR with the luciferase reporters were selected in 100 mg/ml G418. These cells were plated on 96-well plates at 100,000 cells/well and incubated overnight.

For the purification of the TLR5-stimulating activity, saturated L. monocytogenes culture (200 ml of TSB) was centrifuged, and the supernatant was enriched for molecules larger than 30 kDa by ultrafiltration (Ultrafree-15 filter unit with Biomax-30 membrane, Millipore). The buffer was changed to 100 mM Tris pH 7.5, and the volume was adjusted to 5 ml. The sample was loaded onto a HR5/10 reverse-phase chromatography column (AP Biotech) and run at 0.3 ml/min. Reverse-phase chromatography was performed with the indicated elution profile using the following buffers: (A) initial buffer, 0.1% TFA in water, (B) final buffer, 0.1% TFA in acetonitrile. Fractions were collected at 3-minute intervals. FPLC fractions (50 ml) were separated on a 10% SDS-PAGE gel.

As shown in FIG. 3 a, CHO cells expressing an NF-kB luciferase reporter and TLR5 were stimulated with reverse-phase FPLC fractions, and TLR5-mediated NF-kB luciferase activity was measured. The fraction numbers correspond to 3 minute fractions of reverse-phase FPLC eluted with a non-linear gradient of buffer B as shown. Fraction number “N” is control LB growth medium and “P” is the L. monocytogenes culture supernatant prior to chromatography. Fractions containing background activity (1), low activity (2) and high activity (3) as indicated in FIG. 3 a were analyzed by SDS-PAGE and silver stain. Silver staining was performed according to established methods. Two bands with apparent molecular masses of 30-34 kDa were clearly enriched in the fraction containing the highest level of TLR5-stimulating activity (FIG. 3 b, Lane 3). Proteins eluted-from regions A, B, and C of the SDS-PAGE gel, as indicated in FIG. 3 b were assayed for TLR5-mediated NF-kB activation in CHO cells. In FIG. 3 c, “Listeria” indicates L. monocytogenes culture supernatant. One of these bands, (FIG. 3 b, band A), was trypsin-treated, subject to microcapillary HPLC-tandem mass spectrometry, and identified by comparison of peptide tandem mass spectra to sequences in a non redundant protein database using the computer program, SEQUEST27 (FIG. 4 a). TLR5-stimulating activity was not recovered from any other section of the gel. Thus, a TLR5-stimulating activity was purified from culture supernatants from L. monocytogenes.

EXAMPLE IV Flagellin is a TLR5 Stimulus

This example shows that flagellin is a TLR5 stimulus purified from culture supernatants from L. monocytogenes.

As described above, a TLR5-stimulating activity was purified from L. monocytogenes culture supernatants using HPLC. The isolated polypeptide of band A in FIG. 3 b was trypsinized and identified by microcapillary HPLC-tandem mass spectrometry. Peaks corresponding to L. monocytogenes flagellin peptides are indicated in FIG. 4 a. Five sequences were identified (FIG. 4 a) that correspond to flagellin, the product of the flaA gene of L. monocytogenes (Genbank Q02551). The location of these sequences within the protein is indicated in FIG. 4 b. Band B of FIG. 3 b also is flagellin, which migrates as a doublet of approximately 30 kDa on SDS-PAGE (FIG. 3 b).

For analysis, bands A and B were excised from SDS-PAGE gels, dehydrated with acetonitrile, dried under reduced vacuum, and trypsin (12.5 ng/mL) was infused into the gel. The gel slice was allowed to incubate on ice for 45 min in the presence of trypsin and then excess trypsin removed and replaced with 50 mM ammonium bicarbonate and the gel slice incubated overnight at 37° C. Peptides were extracted by 3 washes with 5% acetic acid in 50% aqueous acetonitrile. The extractions were pooled and concentrated by vacuum centrifugation. The peptides were injected onto a C18 peptide trap cartridge (Michrom BioResources, Inc. Auburn, Calif.), desalted, and then injected onto a 75 mm (internal diameter)×10 cm micro-capillary HPLC column (Magic C18; 5-mm packing; 100 A pore size; Michrom BioResources, Inc. Auburn, Calif.). The sample injection was made using a FAMOS autosampler (LCPackings, San Francisco, Calif.) coupled with an Agilent HP 1100 Pump. Peptides were separated by a linear gradient of acetonitrile, and subjected to collision induced dissociation using an electrospray ionization-ion trap mass spectrometer (ESI-ITMS; ThermoQuest, San Jose, Calif.) in data-dependent mode with dynamic exclusion (Goodlett, et al. Anal. Chem. 72, 1112-1118 (2000)). Protein identification was accomplished by use of the SEQUEST computer program (Eng et al., J. Am. Soc. Mass. Spectrom., 5: 976-989 (1994)).

CHO cells expressing an NF-kB luciferase reporter and TLR5 or TLR2 were stimulated with 100 ml/ml Listeria supernatant or 33 mg/ml purified Salmonella flagellin. Flagellin was purified from Salmonella typhimurium (TH4778 fliB− fliC+) by the procedure of Ibrahim et al., J. Clin. Microbiol., 22: 1040-1044 (1985). As shown in FIG. 4 c, flagellin stimulated TLR5-expressing CHO cells, but not TLR2-expressing CHO cells. The mean and standard deviation of quadruplicate samples are indicated. CHO cells were transfected as described in above Examples with the addition of 0.1 mg of pNeo/Tak, and stable populations of cells expressing the indicated TLR with the luciferase reporters were selected in 100 mg/ml G418. These cells were plated on 96-well plates at 100,000 cells/well, incubated overnight, and processed in luciferase assays as described above.

The observation that flagellin is the TLR5 ligand also is supported by the finding that the flagellated bacteria, L. monocytogenes and P. aeruginosa, stimulate TLR5, while the TOP10 strain of E. coli, that has lost its flagella, does not (FIG. 2 b). Similarly, TLR5-stimulating activity was found in B. subtilis, L. innocua, S. typhimurium and S. minnesota, all flagellated bacteria, while non-flagellated bacteria such as H. influenza, did not activate TLR5. Thus, the TLR5-stimulating activity purified from L. monocytogenes culture supernatants was identified as flagellin by tandem mass spectrometry.

EXAMPLE V Flagellin Expression in Bacteria Reconstitutes TLR5-Stimulating Activity

This Example shows that flagellin expression in bacteria reconstitutes TLR-stimulating activity, and deletion of flagellin genes abrogates TLR5-stimulating activity.

To confirm that flagellin is the sole TLR5 ligand in bacteria, E. coli (TOP1O) that secrete little TLR5 activity (FIG. 2 b) were transformed with the cDNA of L. monocytogenes flagellin (flaA) under the control of an inducible promoter. TLR-expressing CHO cells were stimulated for 5 hours with E. coli culture supernatants (67 ml/ml) in which expression of L. monocytogenes flagellin was induced or repressed. In the control sample, CHO cells were stimulated with supernatants from induced E. coli containing the L. monocytogenes flagellin gene cloned in the reverse orientation. Supernatants of E. coli that were induced to express L. monocytogenes flaA contained substantial TLR5-stimulating activity (FIG. 5 a), whereas supernatants from E. coli in which expression was repressed, or from E. coli expressing flaA in the reverse orientation, contained little TLR5 activity in CHO cells expressing an NF-kB luciferase reporter and TLR5 (FIG. 5 a) or TLR2 (FIG. 5 b). CHO cells expressing an NF-kB luciferase reporter and TLR5 (c) or TLR2 (d) were stimulated for 5 hours with culture supernatants (100 ml/ml) from S. typhimurium lacking one copy of flagellin (FliB− fliC+) or both copies of flagellin (FliB+ FliC+). Control is stimulation with LB medium. The mean and standard deviation of quadruplicate samples are indicated.

CHO cells were transfected with TLR2 and TLR5 expression plasmids as described above with the addition of 0.1 mg of pNeo/Tak, and stable populations of cells expressing the indicated TLR with the luciferase reporters were selected in 100 mg/ml G418. These cells were plated on 96-well plates at 100,000 cells/well, incubated overnight, and processed in luciferase assays as described above.

L. monocytogenes flagellin is not recognized by TLR2, since supernatants from E. coli expressing flaA did not show enhanced TLR2-dependent stimulation of CHO cells relative to supernatants from E. coli with repressed flaA expression (FIG. 5 b). In addition to the experiments that demonstrate reconstitution of TLR5-stimulating activity by the expression of flagellin, a bacterium from which flagellin had been deleted was tested. It was observed that TLR5-stimulating activity was abrogated in the flagellin deleted strain. S. typhimurium possess two genes for flagellin, fliB and fliC (Fujita, J., J. Gen Microbiol. 76: 127-34 (1973)). Culture supernatants of fliB− fliC+S. typhimurium contained TLR5-stimulating activity, while culture supernatants from S. typhimurium lacking both flagellins (fliB− fliC−) expressed no TLR5-stimulating activity (FIG. 5 c). The lack of both flagellin genes had no effect on TLR2-stimulating activity (FIG. 5 d). The observed TLR2-stimulating activity found in S. typhimurium supernatants most likely was due to bacterial lipoproteins (Underhill, et al., Nature, 401: 811-5 (1999); Brightbill et al., Science, 285: 732-6 (1999)). These results indicate that flagellin is the sole TLR5-stimulating activity present in S. typhimurium culture supernatant. Thus, TLR5-stimulating activity was elicited by introducing the flagellin gene into a non-flagellated bacterium, and abrogated by deleting the flagellin genes from a flagellated bacterium.

EXAMPLE VI Flagellin-Induced System IL-6 Production in Mice

This example shows that TLR signaling is required for the in vivo immune response to flagellin.

To determine if TLR signaling is required for the in vivo immune response to flagellin, wild type mice and mice lacking a component of the TLR5 signal transduction pathway, MyD88, were injected with flagellin and systemic IL-6 production was monitored. MyD88 is an adaptor protein required for TLR5-mediated signal transduction (Aderem A., et al., Nature, 406: 782-787, (2000); Brightbill, H. D. and Modlin. R. L., Immunology, 101: 1-10, (2000)).

MyD88^(−/−) mice (129/SvJ×C57B1/6 background) were backcrossed for three generations with C57B1/6 mice (Adachi, O. et al., Immunity, 9: 143-150 (1998)). Mice from the F₃ generation (MyD88^(−/−), n=5) and littermate controls (MyD88+/+, n=5) were injected i.p. with 30 mg purified flagellin in 0.5 cc of saline. Blood was sampled at 0, 1, 2, 4 and 8 hours after injection, and IL-6 levels were determined by ELISA (Duoset, R&D Systems, Minneapolis, Minn.).

FIG. 6 shows that flagellin induced systemic IL-6 within 2 h in wile type mice. By contrast, mice deficient in MyD88 were completely unresponsive to flagellin. Therefore, flagellin stimulates TLR5-mediated responses in vivo.

EXAMPLE VII TLR-5 Recognition of a Conserved Site on Flagellin

This example shows that that TLR5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility.

TLR5 Recognizes Evolutionarily Conserved Domain of Flagellin. Flagellin is known to undergo N-methylation of lysine residues, and glycosylation in some bacteria. Using Salmonella typhimurium flagellin expressed in and secreted from Chinese hamster ovary (CHO) cells, we determined that bacteria-specific post-translational modifications of flagellin were not required for TLR5 recognition.

To define the region of the flagellin monomer recognized by TLR5, we made flagellin deletion mutants and tested whether they were able to activate TLR5. Briefly, the D1-99 mutant was made by PCR amplification of S. typhimurium fliC gene (GenBank accession no. D13689 having SEQ ID NO:68) encoding amino acids 100-494, and adding an ATG colon to the 5′ end of the 100-494 coding region. This PCR fragment was cloned into pTrcHIS2 (Invitrogen), and transformed into flagellin-negative (Hayashi, F. et al., Nature, 410:1099-1103 (2001)) TOP10 E. coli cells (Invitrogen). Construction of S. typhimurium BC3-79 strain, and the ptrc fliC:: i31 plasmids were performed by placing fliC::i31 alleles in-frame insertion of an additional 31 codons (non-fliC DNA) into the fliC gene (Manoil, C. et al., J. Mol. Biol., 267: 250-263 (1997)). The unique BarnHI site located within the 31-codon sequence allowed restriction and religation of different ptrcfliC::i31 plasmids to create new plasmids encoding FliC::31 with internal deletions between insertion sites. Bacterial cultures, grown overnight at 37° C. with 50 ug/ml ampicillin and 1 mM IPTG, were probe-sonicated for 60 sec to release and disperse flagellin from bacterial cells.

CHO K1 cells (ATCC) were grown in HAM's F-12 medium with penicillin, streptomycin, L-glutamine and 10% fetal calf serum (HyClone). RAW 264.7 cells were grown in RPMI 1640 with penicillin, streptomycin, L-glutamine and 10% fetal calf serum. NF-kB luciferase reporter assays were preformed as follows: CHO K1 cells were transfected with either the human or mouse TLR5 cDNA cloned into the pEF6 V5/His TOPO vector (Invitrogen), ELAM-LUC (Underhill, et al. Proc. Natl. Acad. Sci. USA, 96: 14459-14463 (1999)) and pRL-TK (Promega) plasmids, selected with blasticidin, and cloned by limiting dilution. Stable clones were stimulated for 4-5 h, and assayed for luciferase activity. All assays were done in triplicate, and each experiment was repeated at least three times. Fold-induction was calculated by dividing the luciferase values for the test conditions by the relative luciferase value for the control condition.

FIG. 8 shows the results of these deletion mutants. In FIG. 8( a) CHO cells expressing human TLR5 and an NF-κB luciferase reporter were stimulated with bacterial sonicates (approximately 10⁸ cells/ml) from cells expressing no flagellin (BC379), WT flagellin, or an N-terminal 100 amino acid flagellin deletion mutant (Δ1-99). Shown is the fold induction of luciferase activity relative control cells (BC379). FIG. 8( b) is an immunoblot of bacterial sonicates from FliC deletion mutants, showing the detection of FliC with rabbit anti-FliC antiserum. FIG. 8( c) shows FliC deletion mutants were tested as in (a) for their TLR5-stimulatory capacity; data shown is representative of at least three independent experiments. FIG. 8( d) illustrates the position of the deletion mutants tested is shown on the ribbon diagram of the flagellin structure (Samatey, F. A. et al., Nature, 410: 331-337 (2001)). In the ribbon diagram of flagellin, the D1 domain consists of the red and blue colored segments, the D2 domain is colored green, and the D3 domain is colored yellow. The overlying green areas designate the deletions that had no effect on TLR5 recognition, and the red areas designate deletions that abrogated TLR5 recognition.

Deletion of the amino-terminal 99 amino acids of the S. typhimurium FliC flagellin monomer prevented TLR5 recognition (FIG. 8 a). There was no detectable stimulation of vector control transfected CHO cells (data not shown). Deletions that removed amino acids 416-444 within the C-terminus of FliC were sufficient to abrogate TLR5 recognition (FIG. 8 b, c and d). These D1 domain polypeptide regions are highly conserved amongst bacteria, and are essential for motility. In contrast, deletion of FliC residues 444-492, within the C-terminal D1 domain, or D3 domain residues 185-306, within the hypervariable domain, had no effect. The D3 domain is exposed at the surface of the flagellar filament, is not required for motility, and is a common target for antibody responses. Its high degree of variability suggests that the D3 domain has evolved to permit considerable structural heterogeneity in order to evade adaptive immune responses.

We refined the TLR5 recognition site using a panel of 23 S. typhimurium fliC transposon insertion mutants. These mutants were generated using a Tn lacZ/in transposon system (Manoil, C., et al., J. Mol. Biol., 267: 250-263 (1997)), which results in the insertion of an in-frame 31 amino acid polypeptide into the flagellin sequence.

The results of this analysis are shown in FIG. 9 and indicate that S. typhimuirium FliC with insertions in the conserved D1 domain after residues 93, 166, 168, 416 and 424, abrogated TLR5 recognition, whereas none of the other 18 insertions had any effect (FIG. 9 c). Briefly, FIG. 9( a) indicates the position of insertions tested on the ribbon diagram of the flagellin structure, with the red area highlighting the cluster of insertions that abrogate TLR5 recognition. FIG. 9( b) is an immunoblot for flagellin demonstrating comparable amounts of S. typhimurium FliC flagellin for the control (WT) and insertion mutants. Insertion mutants shown in FIG. 9( c) were tested as in FIG. 8, using CHO cells expressing human TLR5; data shown is representative of at least three independent experiments. The amount of sonicated bacterial cells used to stimulate approximately 10⁵ CHO cells in a 200 ul volume is indicated in the legend. In combination, these studies mapped the TLR5 recognition site on flagellin to a discrete region in the D1 domain (FIG. 9 a).

The above studies demonstrate that TLR5 recognizes a site on flagellin comprised of amino terminal residues 78-129 and 135-173, and carboxyl-terminal residues 395-444 of SEQ ID NO:68. We compared the amino acid sequences of flagellin molecules from bacteria with known TLR5-stimulatory activity (Ref. 13, 42 and inventor's observations). This narrowed down the conserved regions of flagellin to amino acid residues 79-118, and 408-439 of SEQ ID NO:68 (shown as SEQ ID NO:52 and SEQ ID NO:59 respectively in FIG. 10A). By comparing the aligned sequences, we identified conserved amino acid residues within these regions that were likely to be important for TLR5 recognition. The non-alanine or -glycine residues in these regions were chosen as candidates for energetically important contacts with TLR5 and 22 alanine mutations were made in flagellin. The proteins were purified, quantitated, and analyzed by SDS-PAGE and Coomassie® blue stain to assess their purity (data not shown).

To generate the flagellin alanine mutants, the fliC gene was cloned into the NcoI and HindIII sites of ptrc99a plasmid. Single amino acid mutations were made using a standard PCR mutagenesis strategy (Smith, K. D., et al., PCR Methods Appl., 2: 253-257 (1993)). All mutations were verified by DNA sequencing. The mutant plasmids were transformed into the BC696 (fliB−/fliC−) strain of S. typhimurium SL1344. BC696 was constructed by the method of Datsenko and Wanner (Datsenko, K. A., et al., Proc. Natl. Acad. Sci. USA, 97: 6640-6645 (2000)). Briefly, λ red-mediated recombination was used to replace the fliC gene of S. typhimurium with a cassette encoding Kan^(R) flanked by FLP recognition target (FRT), which was subsequently excised. The same procedure was repeated at the fliB allele to create BC696, which lacks both flagellin genes, which was confirmed by PCR, immunoblot and motility assays. Flagellin mutant protein expression in BC696 transformants was induced by culture in the presence of 1 mM IPTG, and confirmed by immunoblot, using rabbit anti-FliC anti-serum (Difco) and a goat anti-rabbit horse radish peroxidase conjugate secondary (Jackson Immunolabs).

The results of this study are shown in FIG. 10 where panel (a) shows a ClustalW alignment of flagellin protein sequences from TLR5-stimulatory bacteria. Residues that were mutated to alanine are indicated with an arrow (⇓). Dose-response curves demonstrate representative examples of alanine point mutations that had no significant effect on TLR5 recognition (FIG. 10 b), slightly reduced TLR5 recognition (FIG. 10 c) or substantially reduced TLR5 recognition (FIG. 10 d). FIG. 10( e) shows the effective concentration for half-maximal TLR5 stimulation (EC₅₀) which was calculated for each point mutant and plotted as a bar graph. The mean EC₅₀±S.D. was determined from at least 3 independent experiments. An asterisk (*) denotes the mutants with EC₅₀ that were significantly different from WT flagellin.

As shown in FIG. 10 b-d, the individual alanine mutants tested for their ability to stimulate TLR5 were found to segregate into three broad classes: those that had no effect (FIG. 10 b), those that slightly reduced TLR5 recognition (FIG. 10 c), or those that substantially reduced TLR5 recognition (FIG. 10 d). The effective flagellin concentration required for 50% maximal stimulation (EC₅₀) was calculated for each point mutant, using results from at least three independent experiments (FIG. 10 e). Of the 22 alanine mutants, nine did not significantly (p>0.05) affect TLR5 recognition, 3 (N100A, D412A, and R431A) significantly reduced TLR5 recognition by 50-75%.

(p<0.05), and 10 (L88A, Q89A, R90A, L94A, Q97A, E114, I411, L415, T420A, and L425A) significantly (p<0.001) reduced TLR5 recognition by 76-97%. No single mutation completely abrogated TLR5 recognition.

The alanine mutations also were found to affect bacterial motility. Bacterial motility assay were performed as follows. Bacteria were stab-inoculated into the center of motility plates (LB containing 0.3% Agar, with 50 ug/ml ampicillin and 1 mM IPTG). Cultures were incubated upright at 37° C. for 12 h, and then photographed. The relative motility of the bacteria harboring fliC alanine mutants was calculated by measuring the diameter of the bacterial swarm, and dividing this by the diameter for bacteria harboring the plasmid with WT fliC (% WT motility). Motility was scored as scored as follows: ++, WT motility; +, 30-80% WT motility; +/−, 5-30% WT motility; −, <5% WT motility.

Flagellin's amino- and carboxyl-terminal amino acids are evolutionarily conserved, and many of these conserved residues are likely to be important for flagellar filament assembly and bacterial motility. We tested the panel of flagellin alanine mutants for their effect on bacterial motility. Similar to TLR5 recognition, alanine mutants grouped into three classes: three mutations did not alter motility, eight mutations reduced motility, and 11 mutations completely abrogated bacterial motility. The results of this analysis are shown in Table 1.

TABLE 1 Summary of the effect of alanine substitutions in flagellin on bacterial motility and TLR5 recognition. EC₅₀ (ng/ml) EC₅₀ Mutation¹ Motility² TLR5³ Mean (S.D.) p-value WT ++ 3.4 (2.2) fliC-fljB- − E84A − + 5.5 (2.6) 0.086 L89A +/− − 48.0 (21)  <0.001 Q90A* ++ − 14.0 (5.9) <0.001 R91A* − − 25.0 (8.0) <0.001 R93A* + + 4.5 (2.0) 0.400 E94A* + + 1.8 (0.9) 0.225 L95A* − − 29.0 (8.3) <0.001 V97A* + + 2.8 (1.4) 0.626 Q98A* + − 19.0 (6.7) <0.001 N101A* ++ − 7.7 (7.8) 0.044 T103A* + + 4.9 (2.3) 0.303 S105A* − + 4.7 (2.7) 0.394 D108A* − + 3.6 (1.1) 0.916 E115A − − 23.0 (4.4) <0.001 I412A − −− 115.0 (35)  <0.001 D413A − − 8.6 (2.6) <0.001 L416A ++ − 38.0 (13)  <0.001 T421A + − 25.0 (21)  <0.001 R422A − + 3.2 (1.2) 0.851 L426A + − 19.0 (10)  <0.001 Q430A − + 4.2 (1.6) 0.521 R432A − − 12.0 (3.0) <0.001 ¹Residues located in convex intermolecular contact site [Samatey, 2001 #519] are designated with and asterisk (*). ²Bacterial motility is scored as follows: ++, WT motility; +, 30-80% WT motility; +/−, 5-30% WT motility; −, <5% WT motility. ³TLR5 Recognition is noted as follows: +, does not affect TLR5 recognition; −, reduces TLR5 recognition 2-14 fold; −−, reduces TLR5 recognition >30 fold.

The TLR5 recognition site, defined above, is buried within the core of the flagellar filament. This region is also predicted to be involved in axial intermolecular contacts between individual flagellin monomers that form the protofilament. We purified flagellin monomers and filaments from S. typhimurium, and analyzed the protein preparations by SDS-PAGE (FIG. 11 a).

Briefly, purification of bacterial flagellin was performed growing overnight Salmonella typhimurium strain TH4778 (FliB−/FliC+; gift from Dr. Kelly Hughes, University of Washington) or BC696 harboring fliC expression plasmids in LB medium (supplemented with 50 ug/ml ampicillin and 1 mM IPTG for transformed BC696 strains), and pelleted by centrifugation. Cell pellets were washed once in PBS, resuspended in PBS, and sheared for 2 min at high speed in a Waring blender. The sheared suspension was centrifuged for 10 min. at 8000×g, and the supernatant was collected and centrifuged at 100,000×g for 1 h to pellet flagellin filaments. The pellets of flagellin filaments were resuspended in PBS at 4° C. overnight, and centrifuged at 100,000×g for 1 h. This wash step was repeated twice.

Monomeric flagellin was prepared by resuspending the resulting pellet of flagellin filaments in PBS, heated to 70° C. for 15 min, and passed through a 100 kDa molecular weight cut-off filter (Amicon). The resulting flagellin monomers were recovered from the filtrate, protein concentration was determined using the BCA assay (Pierce), and purity was assessed by SDS-PAGE and Coomassie blue staining.

For purification of bacterial flagellin filaments, the preparation of flagellin filaments was extensively dialyzed against PBS using a 300 kDa molecular weight cut-off membrane (Pierce). The resulting flagellin filaments were recovered, and protein concentration was determined using the BCA assay (Pierce), and purity was assessed by SDS-PAGE and Coomassie blue staining.

The electron microscopy studies described below were performed by mounting filamentous flagellin on a carbon-coated grid, negatively stained with tungsten phosphate with subsequent analysis by transmission electron microscopy.

Cross-linking studies were performed by dissolving Dithiobis[succinimidylpropionate] (DSP, Pierce) in DMSO to 25 mM immediately prior to use. Filamentous flagellin (10 mg/ml in PBS) was cross-linked with 1 mM DSP for 30 min at room temperature; the reaction was stopped by adding 50 mM glycine and incubating 15 min at room temperature. Mock-treated samples were incubated with an equal amount of DMSO without DSP. The DSP treated protein was treated with 50 mM DTT for 30 min at 37° C. to cleave the crosslinker. As a control, monomeric flagellin was similarly reacted. The buffer solution for the above reactions was changed back to PBS. Cross-linked and cleaved samples were heated at 70° C. for 15 min to liberate any monomers for biologic assays of TLR5-stimulatory activity.

FIG. 11 shows that TLR5 recognizes monomeric flagellin. FIG. 11( a) is a Coomassie-stained SDS-PAGE gels of monomeric and filamentous flagellin preparations, showing equivalent amounts of the 50 kDa flagellin protein in both preparations. FIG. 11( b) is an electron micrograph of flagellin filaments. FIG. 11( c) shows the results of CHO cells expressing TLR5 that were stimulated with either monomeric or filamentous flagellin. Fold-induction of NF-κB luciferase reporter was calculated for cells stimulated with either the flagellin monomers or filaments to control stimulated cells. FIG. 11( d) is a Coomassie-stained sDs-PAGE gels of monomeric and filamentous flagellin, untreated or treated with cross-linking agent DSP and/or reducing agent DTT, as described in Methods and indicated in the figure. The monomeric flagellin migrates as a 50 kDa protein (lanes 1 and 3). DSP modification of the flagellin monomer results in a slight retardation in gel migration (lanes 2 and 4). The unmodified flagellin filament is dispersed into 50 kDa monomers (lanes 5 and 7) when heated and denatured for SDS-PAGE. DSP cross-linked flagellin filaments form large molecular complexes that cannot enter the gel (lane 6). Reduction of the DSP-crosslinked flagellin filaments with DTT liberates predominantly monomers, with a few higher molecular weight multimers (lane 8). FIG. 11( e) shows the results of CHO cells expressing TLR5 that were stimulated with flagellin filaments that were left untreated, heated for 15 min at 70° C. to depolymerized into monomers, cross-linked with DSP and heated for 15 min at 70° C., or cross-linked with DSP, reduced with DTT, and heated for 15 min at 70° C. Fold-induction of NF-κB luciferase reporter was calculated for the flagellin preparation stimulated cells relative to control stimulated cells. FIG. 11( f) shows the results of CHO cells expressing TLR5 that were stimulated with flagellin monomers that were left untreated, cross-linked with DSP, or cross-linked with DSP and reduced with DTT. Fold-induction of NF-κB luciferase reporter was calculated for cells stimulated with the flagellin preparations relative to control stimulated cells.

The results of the above analysis demonstrate that flagellin filaments migrated as monomers on SDS-PAGE gels, because they were depolymerized by the heating step during preparation for electrophoresis (FIG. 11 a). The filamentous structure was confirmed by electron microscopy (FIG. 11 b). Filamentous flagellin TLR5-stimulatory activity was reduced by 96% compared to monomeric flagellin (FIG. 11 c). Because some monomers were likely to be liberated from the filament during preparation and stimulation, we stabilized the purified filaments by chemical cross-linking with Dithiobis[succinimidylpropionate], DSP. The cross-linked filaments could not be depolymerized, and were unable to enter the gel (FIG. 11 d, lane 6). When the polymerized form of flagellin was stabilized in this manner, TLR5 stimulatory activity was reduced by greater than 99.5% (FIG. 11 e). DSP is a homobifunctional, thiol-cleavable, cross-linking agent. Reduction of this bond with dithiothreitol (DTT) broke the cross-links, liberated monomers and restored the full TLR5 stimulatory activity of flagellin (FIGS. 11 d, lane 8; and 11 e). As a control, flagellin monomers were treated with DSP, and this resulted in a chemically modified monomer whose migration on SDS-PAGE was slightly retarded. This modified monomer retained full biological activity (FIGS. 11 d, lanes 2 and 4; and 11 f). These results demonstrate that monomeric flagellin rather than filamentous flagellin stimulates TLR5, and that the flagellin TLR5 recognition site is inaccessible within the filament.

TLR5 also was demonstrated to physically interact with flagellin. In this regard, we investigated whether flagellin could precipitate TLR5. CHO cells transfected with V5-tagged TLR5 or TLR2 specifically recognize flagellin or bacterial lipopeptide, respectively (FIG. 12 a). Flagellin was purified from S. typhimurium, biotinylated and incubated with either TLR5 or TLR2 transfected CHO cells (FIGS. 12 b and c). Cells were either lysed and then incubated with biotinylated flagellin for 30 min on ice (4° C.) to examine flagellin-TLR interactions in cell lysates, or pre-incubated with biotinylated flagellin (37° C.) for 30 minutes and then lysed to examine flagellin-TLR interactions in intact cells. Biotinylated flagellin and any associated proteins were affinity purified from the lysates with streptavidin beads. Bound proteins were eluted by boiling in SDS-PAGE sample loading buffer, and a immunoblot was done to identify molecules bound to the beads.

Precipitation of TLR5 was performed with biotinylated bacterial flagellin. Briefly, purified flagellin was biotinylated with EZ-Link Sulfo-NHS-LC-Biotin (Pierce) and the buffer was changed back to PBS. CHO cells were transiently transfected with V5-tagged mTLR5, or mTLR2. After 24 hours intact cells were incubated with biotinylated flagellin for 30 min at 37° C., lysed, and nuclei cleared by 5 min centrifugation at 3000×g, or lysed cells were cleared of nuclei, and the cleared lysate was incubated with 10 ug/ml biotinylated flagellin for 30 min at 4° C. The lysates were next incubated with streptavidin agarose for 30 min at 4° C., and the avidin-cleared supernatant was collected. The avidin beads were washed extensively with PBS, and the purified proteins were eluted by boiling in SDS-PAGE loading buffer. Cell equivalent portions of the purification were separated by SDS-PAGE, and the V5-tagged proteins were identified by immunoblot, using the anti-PK antibody (Serotec), and a rabbit anti-mouse horse radish peroxidase secondary (Jackson Immunolabs).

FIG. 12( a) shows CHO K1 cells transfected with either V5-tagged mouse TLR5 or mouse TLR2, and an NF-kB luciferase reporter. Transfected cells were stimulated with medium (control), LPS (100 ng/ml), bacterial lipopeptide (bLP, 300 ng/ml), or FliC (300 ng/ml), and the fold induction of luciferase activity was quantified after 4 h. FIGS. 12( b) and (c) show V5-tagged mouse TLR5 and TLR2 transfected CHO K1 cells incubated biotinylated flagellin either as intact cells for 30 min at 37° C., or as cell lysates for 30 min at 4° C. The lysates (lanes 1 and 4) were next incubated with streptavidin agarose beads for 30 min at 4° C., the avidin beads were collected by centrifugation, and the residual supernatant was collected (avidin-cleared, lanes 2 and 5). The avidin beads were washed extensively (avidin-purified, lanes 3 and 6). Cell equivalent portions were loaded in each lane, and mouse TLR5 and TLR2 were detected by immunoblotting for the V5 epitope tag. CHO TLR5 lysates were also incubated with biotinylated WT or the I411A FliC mutant, precipitated with streptavidin beads, and immunoblotted for the V5 epitope tag (b lanes 7 and 8). Insertion mutants also were tested as described previously using CHO K1 cells expressing human TLR5 (FIG. 12 d) or mouse TLR5 (FIG. 12 e). Data shown is representative of at least three independent experiments. The amount of sonicated bacterial cells used to stimulate approximately 10⁵ CHO cells in a 200 ul volume is indicated on the x-axis. The bacterial cells tested are shown in the legend, and expressed either no FliC (BC379), (WT), the G166 insertion mutant (G166i::31), or the T168 insertion mutant (T168i::31).

The above results demonstrate that TLR5 specifically bound to biotinylated flagellin (FIG. 12 b), whereas no association of flagellin with TLR2 could be demonstrated (FIG. 12 c). In addition, the I411A mutation markedly reduced association of flagellin with TLR5 in cell lysates (FIG. 12 b, lane 8). Because these experiments were done using whole cells, or cell lysates, the possibility remains that additional factors contributed and that the interaction of flagellin and TLR5 was indirect. Although this is possible, we found that mouse and human TLR5 discriminated between different flagellin insertion mutants when transfected into the same cell line (FIGS. 12 d and e). Mouse TLR5 recognized flagellin insertion mutants after residues 166 and 168, whereas human TLR5 did not. The species-specific differences in TLR5 recognition of flagellin suggest that there is a direct interaction between flagellin and TLR5, since any additional factors were common in this experimental system. Flagellar filaments are comprised of monomers of flagellin that stack together to form long protofilaments, 11 of which wrap together to form the filament (Samatey, F. A. et al., Nature, 410: 331-337 (2001)) and (Yonekura, K., et al., Nature, 424: 643-650 (2003)).

Axial interactions occur between the concave surface (residues 56-69, and 132-151) of one monomer and a convex surface (89-107, 315, and 408-409) of the underlying monomer to form the protofilament (Samatey, F. A. et al., Nature, 410: 331-337 (2001)). Overall 10 of the 13 mutations that affect TLR5 recognition also affect motility, 10 of the 19 mutations that affect motility also affect TLR5 recognition, and all mutations that we made in the convex surface reduce motility and/or TLR5 recognition. Eleven residues in this convex surface were not tested because they are non-conserved, alanine or glycine, or have sidechains that are buried (Samatey, F. A. et al., Nature, 410: 331-337 (2001)). Residues involved in TLR5 recognition and motility overlap with the convex surface involved in axial intermolecular contact between monomers in the protofilament. The combination of structural and functional studies demonstrates that residues R90, L94 and Q97 form a central core of the flagellin structure that is critical for protofilament assembly, bacterial motility, as well as TLR5 recognition.

Protofilaments in the flagellar filament have the ability to convert between different helical states (left-handed (L) and right-handed (R)). The ability of the filaments to switch between L and R states is necessary for propulsion and tumbling activity that is generated by counterclockwise or clockwise rotation of the flagellar motor (Berg, H. C., et al., Nature 245: 380-382 (1973)) and (Larsen, S. H., et al., Nature 249: 74-77 (1974)). When all of the filaments are locked into either the L or R state, the flagellum is straight and non-motile (Yamashita, I. et al., Nat. Struct. Biol., 5: 125-132 (1998)). TLR5 recognition and motility are affected by additional mutations that are adjacent to, but outside the convex surface. Many of the mutations in these residues have the most profound effect on bacterial motility. Some of the mutations that lie outside of the axial contact surface may affect this switching function by altering axial intermolecular interactions, as has been shown for a flagellin D107E mutant (Kamiya, R., Asakura, et al., Nature, 286: 628-630 (1980)). Other mutations alter interactions with their lateral partners (Samatey, F. A. et al., Nature, 410: 331-337 (2001)) and (Yonekura, K., et al., Nature, 424: 643-650 (2003)).

The alanine point mutations have a more profound effect on bacterial motility than on TLR5 recognition. Of the 22 mutations, 8 reduce, and 11 completely abrogate bacterial motility. None of the alanine mutations completely abrogates TLR5 recognition, and each of the 13 individual mutations that reduced TLR5 recognition did so by approximately 2-30 fold. This effect on TLR5 recognition was relatively small compared to the respective effect on bacterial motility, and we predict that most individual point mutations will not profoundly reduce innate immune recognition of flagellin. The I411A mutation has the most profound effect on TLR5 recognition. The I411 sidechain is buried in the D1 domain directly under the α-helix containing core residues R90, L94 and Q97, and likely exerts its effect by indirectly altering the conformation of several overlying residues. Thus, TLR5 recognizes a combinatorial surface on flagellin that is determined by the sum of a large group of residues, and is somewhat permissive to variation in amino acid content within this site. The permissive nature of TLR5 recognition of flagellin allows TLR5 to recognize a broad range of bacterial flagellin molecules. In contrast, many point mutations destroy bacterial motility, and thus the structural requirements for flagellar motility are more rigid. These differences may explain why bacteria in general have failed to evade TLR5 recognition. Such a feat would most likely require a very complex series of mutations in at least two discrete sites of the flagellin molecule (the convex/TLR5 site and the concave site) that in sum would destroy TLR5 recognition, and simultaneously compensate for any potential loss in motility.

The above results demonstrate that TLR5 recognizes flagellin monomers rather than filamentous flagellin, as the TLR5 recognition site is not accessible in filaments, and thus flagellin filaments do not induce TLR5 aggregation. TLR5 recognition of monomeric flagellin also has important implications for the recognition of bacterial flagellin during natural infections. Although it is likely that physical forces and chemical factors at the sites of bacterial infection would be capable of liberating monomeric flagellin for TLR5 recognition, in many instances the predominant form of flagellin would be the flagellar filament, which is anchored to the bacterium. This observation indicates that cellular recognition of flagellin requires breaking down the filament to disperse at least a portion of the flagellin into its monomeric form. One means to accomplish this result would be through phagocytosis, where the flagellar filaments would be exposed to an acidic environment that promotes filament depolymerization. In addition, epithelial cells are also capable of recognizing flagellin, and models of polarized epithelia suggest that apical infection of epithelial cells leads to the translocation of flagellin to the basolateral surface, where it is recognized by TLR5 (Gewirtz, A. T., J. Immuno., 167: 1882-1885 (2001)). The apical uptake and basolateral translocation requires that flagellin is attached (as the filament) to a bacterium capable of invading the cell (Gewirtz, A. T. et al., J. Clin. Invest., 105: 79-92 (2000)). Our studies reveal an unrecognized and important step in the flagellin recognition process. During uptake and translocation of flagellin, the filament must undergo depolymerization to afford recognition by TLR5.

Recognition of flagellin by TLR5 also is sensitive; TLR5 can detect flagellin at concentrations of less than 100 fM. In addition, the above results indicate that TLR5 most likely directly interacts with flagellin and that species-specific differences in TLR5 sequence dictate fine specificity for flagellin molecules, as is hypothesized for TLR4 recognition of LPS (Lien, E. et al., J. Clin. Invest. 105: 497-504 (2000); Poltorak, A., et al, Proc. Natl. Acad. Sci. USA, 97: 2163-2167 (2000); and Hajjar, A. M., et al., Nat. Immunol. 3: 354-359 (2002)) and TLR9 recognition of CpG DNA (Bauer, S. et al., Proc. Natl. Acad. Sci. USA, 98: 9237-9242 (2001); and Takeshita, F. et al., J. Immunol., 167: 3555-3558 (2001).

The recognition of flagellin by both plants and mammals suggests that this recognition is an evolutionarily ancient immune adaptation. The protein is recognized in plants by FLS2, a member of a family of resistance genes. Other than sharing the common feature of an extracellular leucine rich repeat (LRR) domain, there is no significant amino acid similarity that suggests an evolutionary relationship between FLS2 and TLR5 (data not shown). Like TLR5, FLS2 utilizes the LRR domain for detecting flagellin, although, TLR5 recognizes a conserved site on flagellin that is structurally distinct from the site recognized by FLS2 (Felix, G., Duran, et al., Plant J., 18: 265-276 (1999)). Thus, plants and animals have independently evolved LRR receptors that recognize bacterial flagellin, and activate host defense mechanisms.

A common prediction for PAMPs is that they are highly conserved and functionally essential, since they resist the evolutionary pressure imposed upon them by immune systems ranging from plants to animals. The above results directly address this prediction, and for the first time substantiate in molecular detail the exquisite ability of the innate immune system to target a microbial structural unit that is functionally required for bacterial fitness. The detailed understanding of the TLR5-flagellin interaction will provide insight into this very specific aspect of host-pathogen interactions, as well as permit rational design of novel immunomodulatory drugs and the engineering of flagellin proteins for vaccination.

Throughout this application various publications have been referenced. The disclosures of these publications in their entireties are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this invention pertains.

Although the invention has been described with reference to the disclosed embodiments, those skilled in the art will readily appreciate that the specific experiments detailed are only illustrative of the invention. It should be understood that various modifications can be made without departing from the spirit of the invention. 

What is claimed is:
 1. A flagellin polypeptide consisting of amino acid sequences found in a flagellin of SEQ ID NO:19 or SEQ ID NO:68, wherein said polypeptide comprises a first peptide sequence consisting of residues 79-118 of SEQ ID NO:68 or residues 79-118 of SEQ ID NO:19 and a second peptide sequence consisting of residues 135-173 of SEQ ID NO:68 or residues 135-173 of SEQ ID NO:19, and a third peptide sequence consisting of residues 408-439 of SEQ ID NO:68 or residues 403-434 of SEQ ID NO:19, arranged in that order and which polypeptide lacks the amino acid sequence of residues 185-306 of SEQ ID NO:68, i.e., residues 185-301 of SEQ ID NO:19, or the amino acid sequence of residues 445-493 of SEQ ID NO:68, i.e., residues 440-488 of SEQ ID NO:19, or lacks both.
 2. A molecule comprising the flagellin polypeptide of claim 1, and a linker joining the first, second and the third peptide sequences.
 3. A molecule comprising the flagellin polypeptide of claim 1, coupled to a targeting ligand.
 4. The molecule of claim 3 wherein the targeting ligand is an antibody-dependent cell cytotoxicity (ADCC) targeting molecule.
 5. The molecule of claim 3, wherein the targeting ligand targets a tumor cell.
 6. The molecule of claim 3, wherein the targeting ligand targets an immune system cell selected from the group consisting of B cells, T cells, monocytes, dendritic cells, and epithelial cells.
 7. A molecule comprising the flagellin polypeptide of claim 1, coupled to a cytotoxic or radioactive compound.
 8. The flagellin polypeptide of claim 1, wherein the polypeptide is detectably labeled.
 9. A screening composition, comprising: (a) a flagellin polypeptide of claim 1, and (b) a TLR5 polypeptide selected from the group consisting of SEQ ID NO:6 and SEQ ID NO:8.
 10. The composition of claim 9, wherein said flagellin polypeptide is detectably labeled.
 11. A method of inducing an antigen-specific immune response in an individual comprising, administering to an individual an effective amount of composition, said composition containing an antigen and the flagellin polypeptide of claim
 1. 12. A method of inducing a TLR5-mediated response, comprising administering to a TLR5-containing cell an effective amount of the flagellin polypeptide of claim
 1. 13. The method of claim 12, wherein said TLR5-mediated response is TLR5-induced increase in an amount of a cytokine selected from the group consisting of TNFα, IL-1 and IL-6, and/or TLR5-induced NF-κβ activity.
 14. A method of inducing a TLR5-mediated immune response in an individual having a proliferative disease or autoimmune disease, comprising administering to said individual an effective amount of the flagellin polypeptide of claim
 1. 15. The method of claim 14, wherein said flagellin polypeptide further comprises an ADCC targeting molecule.
 16. A method of screening for a TLR5 ligand, agonist or antagonist, comprising: (a) contacting a TLR5 with a candidate compound in the presence of the flagellin polypeptide of claim 1 under conditions wherein binding of said flagellin polypeptide to said TLR5 produces a signal; (b) determining the production of said signal in the presence and absence of said candidate compound, and (c) comparing said signal in the presence of said candidate compound with a predetermined signal in the absence of said candidate compound, wherein a difference between said signals in the presence and absence of said candidate compound indicates that said compound is a TLR5 ligand, agonist or antagonist.
 17. The method of claim 16, wherein said predetermined signal is amount of a cytokine selected from the group consisting of TNFα, IL-1 and IL-6, and/or induction of NF-κβ activity. 